From 20cb432c7b0c1a6b6d368d18a521f9f443891d5b Mon Sep 17 00:00:00 2001 From: t-kimber Date: Thu, 2 Sep 2021 14:06:23 +0200 Subject: [PATCH 1/4] update ligand experiments. --- tests/experiments/test_model_ligand_only.sh | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/experiments/test_model_ligand_only.sh b/tests/experiments/test_model_ligand_only.sh index 86be773..7c9bdb8 100644 --- a/tests/experiments/test_model_ligand_only.sh +++ b/tests/experiments/test_model_ligand_only.sh @@ -6,11 +6,11 @@ echo "Models" echo "Ligand only" -# echo "Running model for '001_example-ligand-only-morgan1024-subset'" -# python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-morgan1024-subset.py --overwrite +echo "Running model for '001_example-ligand-only-morgan1024-subset'" +python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-morgan1024-subset.py --overwrite -# echo "Running model for '001_example-ligand-only-smiles-subset.py'" -# python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-smiles-subset.py.py --overwrite +echo "Running model for '001_example-ligand-only-smiles-subset.py'" +python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-smiles-subset.py.py --overwrite -# echo "Running model for '001_example-ligand-only-graph-subset'" -# python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-graph-subset.py --overwrite +echo "Running model for '001_example-ligand-only-graph-subset'" +python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-graph-subset.py --overwrite From 2308beacb7dc7d717ec1a324c561ed90b4571f8a Mon Sep 17 00:00:00 2001 From: t-kimber Date: Thu, 2 Sep 2021 14:07:16 +0200 Subject: [PATCH 2/4] update generated notebooks. --- .../featurize.ipynb | 594 ++++++++-------- .../featurize.ipynb | 538 +++++++-------- .../featurize.ipynb | 638 +++++++++--------- 3 files changed, 888 insertions(+), 882 deletions(-) diff --git a/features/ligand-only-graph-subsample/featurize.ipynb b/features/ligand-only-graph-subsample/featurize.ipynb index b136556..ab3b724 100644 --- a/features/ligand-only-graph-subsample/featurize.ipynb +++ b/features/ligand-only-graph-subsample/featurize.ipynb @@ -4,10 +4,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.014287, - "end_time": "2021-08-16T14:57:22.325579", + "duration": 0.014201, + "end_time": "2021-09-02T11:59:48.496344", "exception": false, - "start_time": "2021-08-16T14:57:22.311292", + "start_time": "2021-09-02T11:59:48.482143", "status": "completed" }, "tags": [] @@ -28,10 +28,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.008386, - "end_time": "2021-08-16T14:57:22.346703", + "duration": 0.006936, + "end_time": "2021-09-02T11:59:48.511318", "exception": false, - "start_time": "2021-08-16T14:57:22.338317", + "start_time": "2021-09-02T11:59:48.504382", "status": "completed" }, "tags": [] @@ -47,16 +47,16 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:22.367109Z", - "iopub.status.busy": "2021-08-16T14:57:22.366500Z", - "iopub.status.idle": "2021-08-16T14:57:22.368216Z", - "shell.execute_reply": "2021-08-16T14:57:22.368761Z" + "iopub.execute_input": "2021-09-02T11:59:48.529878Z", + "iopub.status.busy": "2021-09-02T11:59:48.529242Z", + "iopub.status.idle": "2021-09-02T11:59:48.531227Z", + "shell.execute_reply": "2021-09-02T11:59:48.531669Z" }, "papermill": { - "duration": 0.015324, - "end_time": "2021-08-16T14:57:22.369045", + "duration": 0.014583, + "end_time": "2021-09-02T11:59:48.531922", "exception": false, - "start_time": "2021-08-16T14:57:22.353721", + "start_time": "2021-09-02T11:59:48.517339", "status": "completed" }, "tags": [] @@ -72,10 +72,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005674, - "end_time": "2021-08-16T14:57:22.380373", + "duration": 0.005879, + "end_time": "2021-09-02T11:59:48.543789", "exception": false, - "start_time": "2021-08-16T14:57:22.374699", + "start_time": "2021-09-02T11:59:48.537910", "status": "completed" }, "tags": [] @@ -89,16 +89,16 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:22.397096Z", - "iopub.status.busy": "2021-08-16T14:57:22.396538Z", - "iopub.status.idle": "2021-08-16T14:57:22.398206Z", - "shell.execute_reply": "2021-08-16T14:57:22.398650Z" + "iopub.execute_input": "2021-09-02T11:59:48.560073Z", + "iopub.status.busy": "2021-09-02T11:59:48.559444Z", + "iopub.status.idle": "2021-09-02T11:59:48.561345Z", + "shell.execute_reply": "2021-09-02T11:59:48.561713Z" }, "papermill": { - "duration": 0.012818, - "end_time": "2021-08-16T14:57:22.398816", + "duration": 0.012591, + "end_time": "2021-09-02T11:59:48.561880", "exception": false, - "start_time": "2021-08-16T14:57:22.385998", + "start_time": "2021-09-02T11:59:48.549289", "status": "completed" }, "tags": [ @@ -111,6 +111,8 @@ "DATASET_CLS = \"import.path.to.DatasetProvider\"\n", "DATASET_KWARGS = {\"option\": \"value\", \"option2\": \"value2\"}\n", "\n", + "FEATURIZE_KWARGS = {}\n", + "\n", "PIPELINES = {\n", " \"someuniquekey\": [\n", " (\"import.path.to.SomeFeaturizer\", {\"option\": \"value\", \"option2\": \"value2\"}),\n", @@ -134,19 +136,19 @@ { "cell_type": "code", "execution_count": 3, - "id": "98894966", + "id": "ba28a959", "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:22.414226Z", - "iopub.status.busy": "2021-08-16T14:57:22.413538Z", - "iopub.status.idle": "2021-08-16T14:57:22.415230Z", - "shell.execute_reply": "2021-08-16T14:57:22.415795Z" + "iopub.execute_input": "2021-09-02T11:59:48.577568Z", + "iopub.status.busy": "2021-09-02T11:59:48.576716Z", + "iopub.status.idle": "2021-09-02T11:59:48.578667Z", + "shell.execute_reply": "2021-09-02T11:59:48.579100Z" }, "papermill": { - "duration": 0.011629, - "end_time": "2021-08-16T14:57:22.416017", + "duration": 0.012081, + "end_time": "2021-09-02T11:59:48.579266", "exception": false, - "start_time": "2021-08-16T14:57:22.404388", + "start_time": "2021-09-02T11:59:48.567185", "status": "completed" }, "tags": [ @@ -187,10 +189,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005252, - "end_time": "2021-08-16T14:57:22.426830", + "duration": 0.005368, + "end_time": "2021-09-02T11:59:48.590007", "exception": false, - "start_time": "2021-08-16T14:57:22.421578", + "start_time": "2021-09-02T11:59:48.584639", "status": "completed" }, "tags": [] @@ -208,16 +210,16 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:22.443211Z", - "iopub.status.busy": "2021-08-16T14:57:22.442647Z", - "iopub.status.idle": "2021-08-16T14:57:22.445575Z", - "shell.execute_reply": "2021-08-16T14:57:22.446161Z" + "iopub.execute_input": "2021-09-02T11:59:48.607074Z", + "iopub.status.busy": "2021-09-02T11:59:48.606346Z", + "iopub.status.idle": "2021-09-02T11:59:48.608990Z", + "shell.execute_reply": "2021-09-02T11:59:48.609429Z" }, "papermill": { - "duration": 0.014457, - "end_time": "2021-08-16T14:57:22.446323", + "duration": 0.013794, + "end_time": "2021-09-02T11:59:48.609597", "exception": false, - "start_time": "2021-08-16T14:57:22.431866", + "start_time": "2021-09-02T11:59:48.595803", "status": "completed" }, "tags": [] @@ -264,16 +266,16 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:22.460849Z", - "iopub.status.busy": "2021-08-16T14:57:22.460318Z", - "iopub.status.idle": "2021-08-16T14:57:22.461994Z", - "shell.execute_reply": "2021-08-16T14:57:22.462527Z" + "iopub.execute_input": "2021-09-02T11:59:48.624654Z", + "iopub.status.busy": "2021-09-02T11:59:48.623822Z", + "iopub.status.idle": "2021-09-02T11:59:48.625692Z", + "shell.execute_reply": "2021-09-02T11:59:48.626129Z" }, "papermill": { - "duration": 0.010748, - "end_time": "2021-08-16T14:57:22.462689", + "duration": 0.010915, + "end_time": "2021-09-02T11:59:48.626294", "exception": false, - "start_time": "2021-08-16T14:57:22.451941", + "start_time": "2021-09-02T11:59:48.615379", "status": "completed" }, "tags": [] @@ -288,10 +290,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.00522, - "end_time": "2021-08-16T14:57:22.473674", + "duration": 0.005158, + "end_time": "2021-09-02T11:59:48.637288", "exception": false, - "start_time": "2021-08-16T14:57:22.468454", + "start_time": "2021-09-02T11:59:48.632130", "status": "completed" }, "tags": [] @@ -305,16 +307,16 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:22.488455Z", - "iopub.status.busy": "2021-08-16T14:57:22.487907Z", - "iopub.status.idle": "2021-08-16T14:57:23.153803Z", - "shell.execute_reply": "2021-08-16T14:57:23.154161Z" + "iopub.execute_input": "2021-09-02T11:59:48.651876Z", + "iopub.status.busy": "2021-09-02T11:59:48.651323Z", + "iopub.status.idle": "2021-09-02T11:59:49.332532Z", + "shell.execute_reply": "2021-09-02T11:59:49.333131Z" }, "papermill": { - "duration": 0.675663, - "end_time": "2021-08-16T14:57:23.154429", + "duration": 0.691024, + "end_time": "2021-09-02T11:59:49.333395", "exception": false, - "start_time": "2021-08-16T14:57:22.478766", + "start_time": "2021-09-02T11:59:48.642371", "status": "completed" }, "tags": [] @@ -324,7 +326,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Run started at 2021-08-16 16:57:23.149192\n" + "Run started at 2021-09-02 13:59:49.328655\n" ] } ], @@ -347,10 +349,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005198, - "end_time": "2021-08-16T14:57:23.164978", + "duration": 0.005154, + "end_time": "2021-09-02T11:59:49.344072", "exception": false, - "start_time": "2021-08-16T14:57:23.159780", + "start_time": "2021-09-02T11:59:49.338918", "status": "completed" }, "tags": [] @@ -368,16 +370,16 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:23.179544Z", - "iopub.status.busy": "2021-08-16T14:57:23.179005Z", - "iopub.status.idle": "2021-08-16T14:57:23.987161Z", - "shell.execute_reply": "2021-08-16T14:57:23.984932Z" + "iopub.execute_input": "2021-09-02T11:59:49.358922Z", + "iopub.status.busy": "2021-09-02T11:59:49.358386Z", + "iopub.status.idle": "2021-09-02T11:59:50.177855Z", + "shell.execute_reply": "2021-09-02T11:59:50.175621Z" }, "papermill": { - "duration": 0.816727, - "end_time": "2021-08-16T14:57:23.987313", + "duration": 0.828019, + "end_time": "2021-09-02T11:59:50.178008", "exception": false, - "start_time": "2021-08-16T14:57:23.170586", + "start_time": "2021-09-02T11:59:49.349989", "status": "completed" }, "tags": [] @@ -393,7 +395,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "49ed3511732d44d98cee1dcf6d1c39fe", + "model_id": "83db1a2c4a1742eb98a792fffc1b225e", "version_major": 2, "version_minor": 0 }, @@ -425,16 +427,16 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:24.010750Z", - "iopub.status.busy": "2021-08-16T14:57:24.010209Z", - "iopub.status.idle": "2021-08-16T14:57:24.015679Z", - "shell.execute_reply": "2021-08-16T14:57:24.016248Z" + "iopub.execute_input": "2021-09-02T11:59:50.202183Z", + "iopub.status.busy": "2021-09-02T11:59:50.201230Z", + "iopub.status.idle": "2021-09-02T11:59:50.212717Z", + "shell.execute_reply": "2021-09-02T11:59:50.213054Z" }, "papermill": { - "duration": 0.02325, - "end_time": "2021-08-16T14:57:24.016412", + "duration": 0.02702, + "end_time": "2021-09-02T11:59:50.213224", "exception": false, - "start_time": "2021-08-16T14:57:23.993162", + "start_time": "2021-09-02T11:59:50.186204", "status": "completed" }, "tags": [] @@ -594,10 +596,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005737, - "end_time": "2021-08-16T14:57:24.028054", + "duration": 0.00615, + "end_time": "2021-09-02T11:59:50.225528", "exception": false, - "start_time": "2021-08-16T14:57:24.022317", + "start_time": "2021-09-02T11:59:50.219378", "status": "completed" }, "tags": [] @@ -611,16 +613,16 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:24.045347Z", - "iopub.status.busy": "2021-08-16T14:57:24.044760Z", - "iopub.status.idle": "2021-08-16T14:57:24.049278Z", - "shell.execute_reply": "2021-08-16T14:57:24.049890Z" + "iopub.execute_input": "2021-09-02T11:59:50.243740Z", + "iopub.status.busy": "2021-09-02T11:59:50.242841Z", + "iopub.status.idle": "2021-09-02T11:59:50.247835Z", + "shell.execute_reply": "2021-09-02T11:59:50.248280Z" }, "papermill": { - "duration": 0.016316, - "end_time": "2021-08-16T14:57:24.050116", + "duration": 0.016333, + "end_time": "2021-09-02T11:59:50.248452", "exception": false, - "start_time": "2021-08-16T14:57:24.033800", + "start_time": "2021-09-02T11:59:50.232119", "status": "completed" }, "tags": [] @@ -661,16 +663,16 @@ "execution_count": 10, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:24.066020Z", - "iopub.status.busy": "2021-08-16T14:57:24.065470Z", - "iopub.status.idle": "2021-08-16T14:57:27.027683Z", - "shell.execute_reply": "2021-08-16T14:57:27.028077Z" + "iopub.execute_input": "2021-09-02T11:59:50.265371Z", + "iopub.status.busy": "2021-09-02T11:59:50.264500Z", + "iopub.status.idle": "2021-09-02T11:59:53.183374Z", + "shell.execute_reply": "2021-09-02T11:59:53.183781Z" }, "papermill": { - "duration": 2.971947, - "end_time": "2021-08-16T14:57:27.028257", + "duration": 2.929402, + "end_time": "2021-09-02T11:59:53.183960", "exception": false, - "start_time": "2021-08-16T14:57:24.056310", + "start_time": "2021-09-02T11:59:50.254558", "status": "completed" }, "tags": [] @@ -685,10 +687,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005985, - "end_time": "2021-08-16T14:57:27.040696", + "duration": 0.007117, + "end_time": "2021-09-02T11:59:53.197434", "exception": false, - "start_time": "2021-08-16T14:57:27.034711", + "start_time": "2021-09-02T11:59:53.190317", "status": "completed" }, "tags": [] @@ -701,10 +703,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006293, - "end_time": "2021-08-16T14:57:27.053214", + "duration": 0.00634, + "end_time": "2021-09-02T11:59:53.209892", "exception": false, - "start_time": "2021-08-16T14:57:27.046921", + "start_time": "2021-09-02T11:59:53.203552", "status": "completed" }, "tags": [] @@ -718,16 +720,16 @@ "execution_count": 11, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:27.071320Z", - "iopub.status.busy": "2021-08-16T14:57:27.070491Z", - "iopub.status.idle": "2021-08-16T14:57:27.072544Z", - "shell.execute_reply": "2021-08-16T14:57:27.073093Z" + "iopub.execute_input": "2021-09-02T11:59:53.227649Z", + "iopub.status.busy": "2021-09-02T11:59:53.226691Z", + "iopub.status.idle": "2021-09-02T11:59:53.228758Z", + "shell.execute_reply": "2021-09-02T11:59:53.229134Z" }, "papermill": { - "duration": 0.014186, - "end_time": "2021-08-16T14:57:27.073261", + "duration": 0.013542, + "end_time": "2021-09-02T11:59:53.229301", "exception": false, - "start_time": "2021-08-16T14:57:27.059075", + "start_time": "2021-09-02T11:59:53.215759", "status": "completed" }, "tags": [] @@ -748,10 +750,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006162, - "end_time": "2021-08-16T14:57:27.085451", + "duration": 0.006182, + "end_time": "2021-09-02T11:59:53.242036", "exception": false, - "start_time": "2021-08-16T14:57:27.079289", + "start_time": "2021-09-02T11:59:53.235854", "status": "completed" }, "tags": [] @@ -767,16 +769,16 @@ "execution_count": 12, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:27.103692Z", - "iopub.status.busy": "2021-08-16T14:57:27.103062Z", - "iopub.status.idle": "2021-08-16T14:57:27.105351Z", - "shell.execute_reply": "2021-08-16T14:57:27.105688Z" + "iopub.execute_input": "2021-09-02T11:59:53.260897Z", + "iopub.status.busy": "2021-09-02T11:59:53.260292Z", + "iopub.status.idle": "2021-09-02T11:59:53.262727Z", + "shell.execute_reply": "2021-09-02T11:59:53.263103Z" }, "papermill": { - "duration": 0.014514, - "end_time": "2021-08-16T14:57:27.105855", + "duration": 0.015196, + "end_time": "2021-09-02T11:59:53.263286", "exception": false, - "start_time": "2021-08-16T14:57:27.091341", + "start_time": "2021-09-02T11:59:53.248090", "status": "completed" }, "tags": [] @@ -823,10 +825,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006042, - "end_time": "2021-08-16T14:57:27.117965", + "duration": 0.006322, + "end_time": "2021-09-02T11:59:53.276005", "exception": false, - "start_time": "2021-08-16T14:57:27.111923", + "start_time": "2021-09-02T11:59:53.269683", "status": "completed" }, "tags": [] @@ -849,16 +851,16 @@ "execution_count": 13, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:27.219824Z", - "iopub.status.busy": "2021-08-16T14:57:27.176440Z", - "iopub.status.idle": "2021-08-16T14:57:28.016193Z", - "shell.execute_reply": "2021-08-16T14:57:28.016620Z" + "iopub.execute_input": "2021-09-02T11:59:53.373353Z", + "iopub.status.busy": "2021-09-02T11:59:53.330947Z", + "iopub.status.idle": "2021-09-02T11:59:54.169107Z", + "shell.execute_reply": "2021-09-02T11:59:54.169482Z" }, "papermill": { - "duration": 0.892744, - "end_time": "2021-08-16T14:57:28.016788", + "duration": 0.887665, + "end_time": "2021-09-02T11:59:54.169655", "exception": false, - "start_time": "2021-08-16T14:57:27.124044", + "start_time": "2021-09-02T11:59:53.281990", "status": "completed" }, "tags": [] @@ -882,10 +884,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006217, - "end_time": "2021-08-16T14:57:28.029203", + "duration": 0.0065, + "end_time": "2021-09-02T11:59:54.182609", "exception": false, - "start_time": "2021-08-16T14:57:28.022986", + "start_time": "2021-09-02T11:59:54.176109", "status": "completed" }, "tags": [] @@ -899,16 +901,16 @@ "execution_count": 14, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:28.044693Z", - "iopub.status.busy": "2021-08-16T14:57:28.044125Z", - "iopub.status.idle": "2021-08-16T14:57:28.051404Z", - "shell.execute_reply": "2021-08-16T14:57:28.051795Z" + "iopub.execute_input": "2021-09-02T11:59:54.198477Z", + "iopub.status.busy": "2021-09-02T11:59:54.197941Z", + "iopub.status.idle": "2021-09-02T11:59:54.205132Z", + "shell.execute_reply": "2021-09-02T11:59:54.205661Z" }, "papermill": { - "duration": 0.016829, - "end_time": "2021-08-16T14:57:28.051966", + "duration": 0.017222, + "end_time": "2021-09-02T11:59:54.205901", "exception": false, - "start_time": "2021-08-16T14:57:28.035137", + "start_time": "2021-09-02T11:59:54.188679", "status": "completed" }, "tags": [] @@ -936,16 +938,16 @@ "execution_count": 15, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:28.068701Z", - "iopub.status.busy": "2021-08-16T14:57:28.068124Z", - "iopub.status.idle": "2021-08-16T14:57:28.069749Z", - "shell.execute_reply": "2021-08-16T14:57:28.070205Z" + "iopub.execute_input": "2021-09-02T11:59:54.222057Z", + "iopub.status.busy": "2021-09-02T11:59:54.221516Z", + "iopub.status.idle": "2021-09-02T11:59:54.223331Z", + "shell.execute_reply": "2021-09-02T11:59:54.223780Z" }, "papermill": { - "duration": 0.01174, - "end_time": "2021-08-16T14:57:28.070368", + "duration": 0.011799, + "end_time": "2021-09-02T11:59:54.223946", "exception": false, - "start_time": "2021-08-16T14:57:28.058628", + "start_time": "2021-09-02T11:59:54.212147", "status": "completed" }, "tags": [] @@ -960,16 +962,16 @@ "execution_count": 16, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:28.085804Z", - "iopub.status.busy": "2021-08-16T14:57:28.085226Z", - "iopub.status.idle": "2021-08-16T14:57:28.086905Z", - "shell.execute_reply": "2021-08-16T14:57:28.087448Z" + "iopub.execute_input": "2021-09-02T11:59:54.239709Z", + "iopub.status.busy": "2021-09-02T11:59:54.239173Z", + "iopub.status.idle": "2021-09-02T11:59:54.240599Z", + "shell.execute_reply": "2021-09-02T11:59:54.241172Z" }, "papermill": { - "duration": 0.011003, - "end_time": "2021-08-16T14:57:28.087609", + "duration": 0.011056, + "end_time": "2021-09-02T11:59:54.241336", "exception": false, - "start_time": "2021-08-16T14:57:28.076606", + "start_time": "2021-09-02T11:59:54.230280", "status": "completed" }, "tags": [] @@ -984,16 +986,16 @@ "execution_count": 17, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:28.103849Z", - "iopub.status.busy": "2021-08-16T14:57:28.103026Z", - "iopub.status.idle": "2021-08-16T14:57:28.105159Z", - "shell.execute_reply": "2021-08-16T14:57:28.105539Z" + "iopub.execute_input": "2021-09-02T11:59:54.256635Z", + "iopub.status.busy": "2021-09-02T11:59:54.256104Z", + "iopub.status.idle": "2021-09-02T11:59:54.257905Z", + "shell.execute_reply": "2021-09-02T11:59:54.258473Z" }, "papermill": { - "duration": 0.011932, - "end_time": "2021-08-16T14:57:28.105795", + "duration": 0.011119, + "end_time": "2021-09-02T11:59:54.258640", "exception": false, - "start_time": "2021-08-16T14:57:28.093863", + "start_time": "2021-09-02T11:59:54.247521", "status": "completed" }, "tags": [] @@ -1008,16 +1010,16 @@ "execution_count": 18, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:28.122408Z", - "iopub.status.busy": "2021-08-16T14:57:28.121689Z", - "iopub.status.idle": "2021-08-16T14:57:28.123853Z", - "shell.execute_reply": "2021-08-16T14:57:28.124226Z" + "iopub.execute_input": "2021-09-02T11:59:54.274423Z", + "iopub.status.busy": "2021-09-02T11:59:54.273882Z", + "iopub.status.idle": "2021-09-02T11:59:54.275941Z", + "shell.execute_reply": "2021-09-02T11:59:54.276309Z" }, "papermill": { - "duration": 0.012166, - "end_time": "2021-08-16T14:57:28.124439", + "duration": 0.011497, + "end_time": "2021-09-02T11:59:54.276477", "exception": false, - "start_time": "2021-08-16T14:57:28.112273", + "start_time": "2021-09-02T11:59:54.264980", "status": "completed" }, "tags": [] @@ -1027,7 +1029,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Run finished at 2021-08-16 16:57:28.120624\n" + "Run finished at 2021-09-02 13:59:54.272782\n" ] } ], @@ -1039,10 +1041,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006429, - "end_time": "2021-08-16T14:57:28.137433", + "duration": 0.006232, + "end_time": "2021-09-02T11:59:54.289141", "exception": false, - "start_time": "2021-08-16T14:57:28.131004", + "start_time": "2021-09-02T11:59:54.282909", "status": "completed" }, "tags": [] @@ -1056,16 +1058,16 @@ "execution_count": 19, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:28.153424Z", - "iopub.status.busy": "2021-08-16T14:57:28.152801Z", - "iopub.status.idle": "2021-08-16T14:57:28.154401Z", - "shell.execute_reply": "2021-08-16T14:57:28.154927Z" + "iopub.execute_input": "2021-09-02T11:59:54.307419Z", + "iopub.status.busy": "2021-09-02T11:59:54.306742Z", + "iopub.status.idle": "2021-09-02T11:59:54.308625Z", + "shell.execute_reply": "2021-09-02T11:59:54.309082Z" }, "papermill": { - "duration": 0.011299, - "end_time": "2021-08-16T14:57:28.155090", + "duration": 0.011686, + "end_time": "2021-09-02T11:59:54.309251", "exception": false, - "start_time": "2021-08-16T14:57:28.143791", + "start_time": "2021-09-02T11:59:54.297565", "status": "completed" }, "tags": [] @@ -1081,16 +1083,16 @@ "execution_count": 20, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:28.171709Z", - "iopub.status.busy": "2021-08-16T14:57:28.171172Z", - "iopub.status.idle": "2021-08-16T14:57:30.661304Z", - "shell.execute_reply": "2021-08-16T14:57:30.661941Z" + "iopub.execute_input": "2021-09-02T11:59:54.326131Z", + "iopub.status.busy": "2021-09-02T11:59:54.325537Z", + "iopub.status.idle": "2021-09-02T11:59:56.820158Z", + "shell.execute_reply": "2021-09-02T11:59:56.820866Z" }, "papermill": { - "duration": 2.500406, - "end_time": "2021-08-16T14:57:30.662132", + "duration": 2.505108, + "end_time": "2021-09-02T11:59:56.821073", "exception": false, - "start_time": "2021-08-16T14:57:28.161726", + "start_time": "2021-09-02T11:59:54.315965", "status": "completed" }, "tags": [] @@ -1102,7 +1104,7 @@ "text": [ "Watermark\n", "---------\n", - "Last updated: 2021-08-16T16:57:28.179422+02:00\n", + "Last updated: 2021-09-02T13:59:54.333680+02:00\n", "\n", "Python implementation: CPython\n", "Python version : 3.8.8\n", @@ -1116,14 +1118,14 @@ "CPU cores : 8\n", "Architecture: 64bit\n", "\n", - "Hostname: Talias-MBP.fritz.box\n", + "Hostname: Talias-MacBook-Pro.local\n", "\n", - "Git hash: 9b0bf29d81be3382d2fb1c08652fedd0cc38bd83\n", + "Git hash: 66e9d900aec806992ec40ac8180bd45f5e1b1512\n", "\n", "sys : 3.8.8 | packaged by conda-forge | (default, Feb 20 2021, 16:12:38) \n", "[Clang 11.0.1 ]\n", - "numpy : 1.20.2\n", "awkward: 1.2.3\n", + "numpy : 1.20.2\n", "\n", "Watermark: 2.2.0\n", "\n", @@ -1272,7 +1274,7 @@ "jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge\n", "jupyterlab_server 2.5.0 pyhd8ed1ab_0 conda-forge\n", "jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge\n", - "kinoml 0+untagged.632.gcb52174 dev_0 \n", + "kinoml 0+untagged.643.g6293842.dirty dev_0 \n", "kiwisolver 1.3.1 py38hd9c93a9_1 conda-forge\n", "klifs-utils 0+unknown pypi_0 pypi\n", "krb5 1.17.2 h60d9502_0 conda-forge\n", @@ -1488,16 +1490,16 @@ "execution_count": 21, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:30.685073Z", - "iopub.status.busy": "2021-08-16T14:57:30.682834Z", - "iopub.status.idle": "2021-08-16T14:57:33.130248Z", - "shell.execute_reply": "2021-08-16T14:57:33.130788Z" + "iopub.execute_input": "2021-09-02T11:59:56.844129Z", + "iopub.status.busy": "2021-09-02T11:59:56.843570Z", + "iopub.status.idle": "2021-09-02T11:59:59.337654Z", + "shell.execute_reply": "2021-09-02T11:59:59.338214Z" }, "papermill": { - "duration": 2.460786, - "end_time": "2021-08-16T14:57:33.130990", + "duration": 2.50868, + "end_time": "2021-09-02T11:59:59.338421", "exception": false, - "start_time": "2021-08-16T14:57:30.670204", + "start_time": "2021-09-02T11:59:56.829741", "status": "completed" }, "tags": [] @@ -1513,16 +1515,16 @@ "execution_count": 22, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:33.150257Z", - "iopub.status.busy": "2021-08-16T14:57:33.149534Z", - "iopub.status.idle": "2021-08-16T14:57:33.153375Z", - "shell.execute_reply": "2021-08-16T14:57:33.152898Z" + "iopub.execute_input": "2021-09-02T11:59:59.360058Z", + "iopub.status.busy": "2021-09-02T11:59:59.359336Z", + "iopub.status.idle": "2021-09-02T11:59:59.361972Z", + "shell.execute_reply": "2021-09-02T11:59:59.362358Z" }, "papermill": { - "duration": 0.014676, - "end_time": "2021-08-16T14:57:33.153527", + "duration": 0.015653, + "end_time": "2021-09-02T11:59:59.362530", "exception": false, - "start_time": "2021-08-16T14:57:33.138851", + "start_time": "2021-09-02T11:59:59.346877", "status": "completed" }, "tags": [] @@ -1541,7 +1543,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -1559,8 +1561,8 @@ }, "papermill": { "default_parameters": {}, - "duration": 13.265184, - "end_time": "2021-08-16T14:57:34.452569", + "duration": 13.274702, + "end_time": "2021-09-02T12:00:00.618202", "environment_variables": {}, "exception": null, "input_path": "features/featurize-template.ipynb", @@ -1608,28 +1610,29 @@ "idx_val": 0.1 } }, - "start_time": "2021-08-16T14:57:21.187385", + "start_time": "2021-09-02T11:59:47.343500", "version": "2.2.0" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": { - "350e462be6a74b5e8e2d879fe1d72d7f": { + "0686588b698a417a8520257e4622a868": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", - "model_name": "DescriptionStyleModel", + "model_name": "ProgressStyleModel", "state": { "_model_module": "@jupyter-widgets/controls", "_model_module_version": "1.5.0", - "_model_name": "DescriptionStyleModel", + "_model_name": "ProgressStyleModel", "_view_count": null, "_view_module": "@jupyter-widgets/base", "_view_module_version": "1.2.0", "_view_name": "StyleView", + "bar_color": null, "description_width": "" } }, - "425710bd9e734a9b83e00151e6600c89": { + "2c89abef799d4e4eb232e2a3f943ccc0": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1681,29 +1684,43 @@ "width": null } }, - "49ed3511732d44d98cee1dcf6d1c39fe": { + "4c9652f2b78b4c339e9e4085e26ef1da": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", - "model_name": "HBoxModel", + "model_name": "DescriptionStyleModel", + "state": { + "_model_module": "@jupyter-widgets/controls", + "_model_module_version": "1.5.0", + "_model_name": "DescriptionStyleModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/base", + "_view_module_version": "1.2.0", + "_view_name": "StyleView", + "description_width": "" + } + }, + "4dc9f649a73f49e1a9486658b67d4793": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "HTMLModel", "state": { "_dom_classes": [], "_model_module": "@jupyter-widgets/controls", "_model_module_version": "1.5.0", - "_model_name": "HBoxModel", + "_model_name": "HTMLModel", "_view_count": null, "_view_module": "@jupyter-widgets/controls", "_view_module_version": "1.5.0", - "_view_name": "HBoxView", - "box_style": "", - "children": [ - "IPY_MODEL_e0fbfd47aae94ad79972690874e828b0", - "IPY_MODEL_971de92b5d27480d9fd88862cc2fee9d", - "IPY_MODEL_c2aa81a0816e4e5690c7d60ca602bcc1" - ], - "layout": "IPY_MODEL_9ebc036ad9c54aa1bde62ced70ec6d52" + "_view_name": "HTMLView", + "description": "", + "description_tooltip": null, + "layout": "IPY_MODEL_2c89abef799d4e4eb232e2a3f943ccc0", + "placeholder": "​", + "style": "IPY_MODEL_4c9652f2b78b4c339e9e4085e26ef1da", + "value": " 100/100 [00:00<00:00, 4173.81it/s]" } }, - "6a42db83e2764f1a996433289f743452": { + "5069a057b70444b991ed41c4ab74ab7c": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", "model_name": "DescriptionStyleModel", @@ -1718,7 +1735,31 @@ "description_width": "" } }, - "8511397122ca45218699f38dcc9b2d9b": { + "5da7e357f04a44cb919ad2977a78163f": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "FloatProgressModel", + "state": { + "_dom_classes": [], + "_model_module": "@jupyter-widgets/controls", + "_model_module_version": "1.5.0", + "_model_name": "FloatProgressModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/controls", + "_view_module_version": "1.5.0", + "_view_name": "ProgressView", + "bar_style": "success", + "description": "", + "description_tooltip": null, + "layout": "IPY_MODEL_868b610f1a2949d0b1de5e13cf7ad6b1", + "max": 100.0, + "min": 0.0, + "orientation": "horizontal", + "style": "IPY_MODEL_0686588b698a417a8520257e4622a868", + "value": 100.0 + } + }, + "763ebc300133446f94a829d559081b47": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1770,31 +1811,29 @@ "width": null } }, - "971de92b5d27480d9fd88862cc2fee9d": { + "83db1a2c4a1742eb98a792fffc1b225e": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", - "model_name": "FloatProgressModel", + "model_name": "HBoxModel", "state": { "_dom_classes": [], "_model_module": "@jupyter-widgets/controls", "_model_module_version": "1.5.0", - "_model_name": "FloatProgressModel", + "_model_name": "HBoxModel", "_view_count": null, "_view_module": "@jupyter-widgets/controls", "_view_module_version": "1.5.0", - "_view_name": "ProgressView", - "bar_style": "success", - "description": "", - "description_tooltip": null, - "layout": "IPY_MODEL_f33e2cb1d2a64c4f86c8a57ffeac1518", - "max": 100.0, - "min": 0.0, - "orientation": "horizontal", - "style": "IPY_MODEL_f0ccb170466243a49742be88dcbbff92", - "value": 100.0 + "_view_name": "HBoxView", + "box_style": "", + "children": [ + "IPY_MODEL_d5dd4d93a1594a6c8c7d947a41d9bd05", + "IPY_MODEL_5da7e357f04a44cb919ad2977a78163f", + "IPY_MODEL_4dc9f649a73f49e1a9486658b67d4793" + ], + "layout": "IPY_MODEL_c7cf6e087c0d4bf48108f5d5e7e6ac2e" } }, - "9ebc036ad9c54aa1bde62ced70ec6d52": { + "868b610f1a2949d0b1de5e13cf7ad6b1": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1846,65 +1885,7 @@ "width": null } }, - "c2aa81a0816e4e5690c7d60ca602bcc1": { - "model_module": "@jupyter-widgets/controls", - "model_module_version": "1.5.0", - "model_name": "HTMLModel", - "state": { - "_dom_classes": [], - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "HTMLModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/controls", - "_view_module_version": "1.5.0", - "_view_name": "HTMLView", - "description": "", - "description_tooltip": null, - "layout": "IPY_MODEL_8511397122ca45218699f38dcc9b2d9b", - "placeholder": "​", - "style": "IPY_MODEL_350e462be6a74b5e8e2d879fe1d72d7f", - "value": " 100/100 [00:00<00:00, 4122.69it/s]" - } - }, - "e0fbfd47aae94ad79972690874e828b0": { - "model_module": "@jupyter-widgets/controls", - "model_module_version": "1.5.0", - "model_name": "HTMLModel", - "state": { - "_dom_classes": [], - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "HTMLModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/controls", - "_view_module_version": "1.5.0", - "_view_name": "HTMLView", - "description": "", - "description_tooltip": null, - "layout": "IPY_MODEL_425710bd9e734a9b83e00151e6600c89", - "placeholder": "​", - "style": "IPY_MODEL_6a42db83e2764f1a996433289f743452", - "value": "100%" - } - }, - "f0ccb170466243a49742be88dcbbff92": { - "model_module": "@jupyter-widgets/controls", - "model_module_version": "1.5.0", - "model_name": "ProgressStyleModel", - "state": { - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "ProgressStyleModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/base", - "_view_module_version": "1.2.0", - "_view_name": "StyleView", - "bar_color": null, - "description_width": "" - } - }, - "f33e2cb1d2a64c4f86c8a57ffeac1518": { + "c7cf6e087c0d4bf48108f5d5e7e6ac2e": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1955,6 +1936,27 @@ "visibility": null, "width": null } + }, + "d5dd4d93a1594a6c8c7d947a41d9bd05": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "HTMLModel", + "state": { + "_dom_classes": [], + "_model_module": "@jupyter-widgets/controls", + "_model_module_version": "1.5.0", + "_model_name": "HTMLModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/controls", + "_view_module_version": "1.5.0", + "_view_name": "HTMLView", + "description": "", + "description_tooltip": null, + "layout": "IPY_MODEL_763ebc300133446f94a829d559081b47", + "placeholder": "​", + "style": "IPY_MODEL_5069a057b70444b991ed41c4ab74ab7c", + "value": "100%" + } } }, "version_major": 2, diff --git a/features/ligand-only-morgan1024-subsample/featurize.ipynb b/features/ligand-only-morgan1024-subsample/featurize.ipynb index 2f412a7..1ad12ad 100644 --- a/features/ligand-only-morgan1024-subsample/featurize.ipynb +++ b/features/ligand-only-morgan1024-subsample/featurize.ipynb @@ -4,10 +4,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.013915, - "end_time": "2021-08-16T14:56:54.011758", + "duration": 0.013608, + "end_time": "2021-09-02T11:59:15.514582", "exception": false, - "start_time": "2021-08-16T14:56:53.997843", + "start_time": "2021-09-02T11:59:15.500974", "status": "completed" }, "tags": [] @@ -28,10 +28,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006686, - "end_time": "2021-08-16T14:56:54.026375", + "duration": 0.006952, + "end_time": "2021-09-02T11:59:15.529570", "exception": false, - "start_time": "2021-08-16T14:56:54.019689", + "start_time": "2021-09-02T11:59:15.522618", "status": "completed" }, "tags": [] @@ -47,16 +47,16 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:54.044556Z", - "iopub.status.busy": "2021-08-16T14:56:54.043940Z", - "iopub.status.idle": "2021-08-16T14:56:54.045782Z", - "shell.execute_reply": "2021-08-16T14:56:54.046322Z" + "iopub.execute_input": "2021-09-02T11:59:15.549294Z", + "iopub.status.busy": "2021-09-02T11:59:15.548723Z", + "iopub.status.idle": "2021-09-02T11:59:15.550692Z", + "shell.execute_reply": "2021-09-02T11:59:15.551245Z" }, "papermill": { - "duration": 0.014357, - "end_time": "2021-08-16T14:56:54.046551", + "duration": 0.015677, + "end_time": "2021-09-02T11:59:15.551537", "exception": false, - "start_time": "2021-08-16T14:56:54.032194", + "start_time": "2021-09-02T11:59:15.535860", "status": "completed" }, "tags": [] @@ -72,10 +72,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.00548, - "end_time": "2021-08-16T14:56:54.057842", + "duration": 0.005734, + "end_time": "2021-09-02T11:59:15.562950", "exception": false, - "start_time": "2021-08-16T14:56:54.052362", + "start_time": "2021-09-02T11:59:15.557216", "status": "completed" }, "tags": [] @@ -89,16 +89,16 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:54.074281Z", - "iopub.status.busy": "2021-08-16T14:56:54.073556Z", - "iopub.status.idle": "2021-08-16T14:56:54.075706Z", - "shell.execute_reply": "2021-08-16T14:56:54.076063Z" + "iopub.execute_input": "2021-09-02T11:59:15.578903Z", + "iopub.status.busy": "2021-09-02T11:59:15.578334Z", + "iopub.status.idle": "2021-09-02T11:59:15.580328Z", + "shell.execute_reply": "2021-09-02T11:59:15.580704Z" }, "papermill": { - "duration": 0.013476, - "end_time": "2021-08-16T14:56:54.076226", + "duration": 0.012967, + "end_time": "2021-09-02T11:59:15.580901", "exception": false, - "start_time": "2021-08-16T14:56:54.062750", + "start_time": "2021-09-02T11:59:15.567934", "status": "completed" }, "tags": [ @@ -111,6 +111,8 @@ "DATASET_CLS = \"import.path.to.DatasetProvider\"\n", "DATASET_KWARGS = {\"option\": \"value\", \"option2\": \"value2\"}\n", "\n", + "FEATURIZE_KWARGS = {}\n", + "\n", "PIPELINES = {\n", " \"someuniquekey\": [\n", " (\"import.path.to.SomeFeaturizer\", {\"option\": \"value\", \"option2\": \"value2\"}),\n", @@ -134,19 +136,19 @@ { "cell_type": "code", "execution_count": 3, - "id": "b876a110", + "id": "a3041823", "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:54.091402Z", - "iopub.status.busy": "2021-08-16T14:56:54.090856Z", - "iopub.status.idle": "2021-08-16T14:56:54.092742Z", - "shell.execute_reply": "2021-08-16T14:56:54.093175Z" + "iopub.execute_input": "2021-09-02T11:59:15.596040Z", + "iopub.status.busy": "2021-09-02T11:59:15.595497Z", + "iopub.status.idle": "2021-09-02T11:59:15.597315Z", + "shell.execute_reply": "2021-09-02T11:59:15.597914Z" }, "papermill": { - "duration": 0.011814, - "end_time": "2021-08-16T14:56:54.093340", + "duration": 0.011793, + "end_time": "2021-09-02T11:59:15.598080", "exception": false, - "start_time": "2021-08-16T14:56:54.081526", + "start_time": "2021-09-02T11:59:15.586287", "status": "completed" }, "tags": [ @@ -190,10 +192,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005225, - "end_time": "2021-08-16T14:56:54.103898", + "duration": 0.005577, + "end_time": "2021-09-02T11:59:15.608998", "exception": false, - "start_time": "2021-08-16T14:56:54.098673", + "start_time": "2021-09-02T11:59:15.603421", "status": "completed" }, "tags": [] @@ -211,16 +213,16 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:54.120465Z", - "iopub.status.busy": "2021-08-16T14:56:54.119883Z", - "iopub.status.idle": "2021-08-16T14:56:54.122243Z", - "shell.execute_reply": "2021-08-16T14:56:54.122781Z" + "iopub.execute_input": "2021-09-02T11:59:15.627225Z", + "iopub.status.busy": "2021-09-02T11:59:15.626653Z", + "iopub.status.idle": "2021-09-02T11:59:15.629470Z", + "shell.execute_reply": "2021-09-02T11:59:15.629975Z" }, "papermill": { - "duration": 0.013771, - "end_time": "2021-08-16T14:56:54.123003", + "duration": 0.014851, + "end_time": "2021-09-02T11:59:15.630151", "exception": false, - "start_time": "2021-08-16T14:56:54.109232", + "start_time": "2021-09-02T11:59:15.615300", "status": "completed" }, "tags": [] @@ -267,16 +269,16 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:54.138177Z", - "iopub.status.busy": "2021-08-16T14:56:54.137567Z", - "iopub.status.idle": "2021-08-16T14:56:54.139456Z", - "shell.execute_reply": "2021-08-16T14:56:54.140073Z" + "iopub.execute_input": "2021-09-02T11:59:15.644777Z", + "iopub.status.busy": "2021-09-02T11:59:15.644231Z", + "iopub.status.idle": "2021-09-02T11:59:15.645995Z", + "shell.execute_reply": "2021-09-02T11:59:15.646425Z" }, "papermill": { - "duration": 0.011706, - "end_time": "2021-08-16T14:56:54.140260", + "duration": 0.010836, + "end_time": "2021-09-02T11:59:15.646595", "exception": false, - "start_time": "2021-08-16T14:56:54.128554", + "start_time": "2021-09-02T11:59:15.635759", "status": "completed" }, "tags": [] @@ -291,10 +293,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005391, - "end_time": "2021-08-16T14:56:54.152103", + "duration": 0.005136, + "end_time": "2021-09-02T11:59:15.657286", "exception": false, - "start_time": "2021-08-16T14:56:54.146712", + "start_time": "2021-09-02T11:59:15.652150", "status": "completed" }, "tags": [] @@ -308,16 +310,16 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:54.167064Z", - "iopub.status.busy": "2021-08-16T14:56:54.166502Z", - "iopub.status.idle": "2021-08-16T14:56:54.820911Z", - "shell.execute_reply": "2021-08-16T14:56:54.821502Z" + "iopub.execute_input": "2021-09-02T11:59:15.671901Z", + "iopub.status.busy": "2021-09-02T11:59:15.671360Z", + "iopub.status.idle": "2021-09-02T11:59:16.773515Z", + "shell.execute_reply": "2021-09-02T11:59:16.774026Z" }, "papermill": { - "duration": 0.664101, - "end_time": "2021-08-16T14:56:54.821676", + "duration": 1.111673, + "end_time": "2021-09-02T11:59:16.774245", "exception": false, - "start_time": "2021-08-16T14:56:54.157575", + "start_time": "2021-09-02T11:59:15.662572", "status": "completed" }, "tags": [] @@ -327,7 +329,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Run started at 2021-08-16 16:56:54.816886\n" + "Run started at 2021-09-02 13:59:16.769063\n" ] } ], @@ -350,10 +352,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005301, - "end_time": "2021-08-16T14:56:54.832476", + "duration": 0.012633, + "end_time": "2021-09-02T11:59:16.806980", "exception": false, - "start_time": "2021-08-16T14:56:54.827175", + "start_time": "2021-09-02T11:59:16.794347", "status": "completed" }, "tags": [] @@ -371,16 +373,16 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:54.855588Z", - "iopub.status.busy": "2021-08-16T14:56:54.854971Z", - "iopub.status.idle": "2021-08-16T14:56:55.660848Z", - "shell.execute_reply": "2021-08-16T14:56:55.658598Z" + "iopub.execute_input": "2021-09-02T11:59:16.826230Z", + "iopub.status.busy": "2021-09-02T11:59:16.825554Z", + "iopub.status.idle": "2021-09-02T11:59:18.416039Z", + "shell.execute_reply": "2021-09-02T11:59:18.413781Z" }, "papermill": { - "duration": 0.81725, - "end_time": "2021-08-16T14:56:55.661002", + "duration": 1.600883, + "end_time": "2021-09-02T11:59:18.416193", "exception": false, - "start_time": "2021-08-16T14:56:54.843752", + "start_time": "2021-09-02T11:59:16.815310", "status": "completed" }, "tags": [] @@ -396,7 +398,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "807c106b126b49ac8c33cb8046ea7784", + "model_id": "55278e51bbba4657b736a6c8be920c4e", "version_major": 2, "version_minor": 0 }, @@ -428,16 +430,16 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:55.680523Z", - "iopub.status.busy": "2021-08-16T14:56:55.679976Z", - "iopub.status.idle": "2021-08-16T14:56:55.689596Z", - "shell.execute_reply": "2021-08-16T14:56:55.690096Z" + "iopub.execute_input": "2021-09-02T11:59:18.435532Z", + "iopub.status.busy": "2021-09-02T11:59:18.434993Z", + "iopub.status.idle": "2021-09-02T11:59:18.444573Z", + "shell.execute_reply": "2021-09-02T11:59:18.445026Z" }, "papermill": { - "duration": 0.023471, - "end_time": "2021-08-16T14:56:55.690263", + "duration": 0.023211, + "end_time": "2021-09-02T11:59:18.445202", "exception": false, - "start_time": "2021-08-16T14:56:55.666792", + "start_time": "2021-09-02T11:59:18.421991", "status": "completed" }, "tags": [] @@ -597,10 +599,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006032, - "end_time": "2021-08-16T14:56:55.702248", + "duration": 0.005746, + "end_time": "2021-09-02T11:59:18.457129", "exception": false, - "start_time": "2021-08-16T14:56:55.696216", + "start_time": "2021-09-02T11:59:18.451383", "status": "completed" }, "tags": [] @@ -614,16 +616,16 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:55.718589Z", - "iopub.status.busy": "2021-08-16T14:56:55.717945Z", - "iopub.status.idle": "2021-08-16T14:56:55.722071Z", - "shell.execute_reply": "2021-08-16T14:56:55.722438Z" + "iopub.execute_input": "2021-09-02T11:59:18.473541Z", + "iopub.status.busy": "2021-09-02T11:59:18.472927Z", + "iopub.status.idle": "2021-09-02T11:59:18.480461Z", + "shell.execute_reply": "2021-09-02T11:59:18.480901Z" }, "papermill": { - "duration": 0.014471, - "end_time": "2021-08-16T14:56:55.722603", + "duration": 0.018277, + "end_time": "2021-09-02T11:59:18.481130", "exception": false, - "start_time": "2021-08-16T14:56:55.708132", + "start_time": "2021-09-02T11:59:18.462853", "status": "completed" }, "tags": [] @@ -664,16 +666,16 @@ "execution_count": 10, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:55.737773Z", - "iopub.status.busy": "2021-08-16T14:56:55.737243Z", - "iopub.status.idle": "2021-08-16T14:56:58.722590Z", - "shell.execute_reply": "2021-08-16T14:56:58.723008Z" + "iopub.execute_input": "2021-09-02T11:59:18.498732Z", + "iopub.status.busy": "2021-09-02T11:59:18.498032Z", + "iopub.status.idle": "2021-09-02T11:59:21.806089Z", + "shell.execute_reply": "2021-09-02T11:59:21.806488Z" }, "papermill": { - "duration": 2.994653, - "end_time": "2021-08-16T14:56:58.723179", + "duration": 3.319639, + "end_time": "2021-09-02T11:59:21.806671", "exception": false, - "start_time": "2021-08-16T14:56:55.728526", + "start_time": "2021-09-02T11:59:18.487032", "status": "completed" }, "tags": [] @@ -688,10 +690,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005687, - "end_time": "2021-08-16T14:56:58.734752", + "duration": 0.00607, + "end_time": "2021-09-02T11:59:21.819539", "exception": false, - "start_time": "2021-08-16T14:56:58.729065", + "start_time": "2021-09-02T11:59:21.813469", "status": "completed" }, "tags": [] @@ -704,10 +706,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005852, - "end_time": "2021-08-16T14:56:58.746358", + "duration": 0.006171, + "end_time": "2021-09-02T11:59:21.831614", "exception": false, - "start_time": "2021-08-16T14:56:58.740506", + "start_time": "2021-09-02T11:59:21.825443", "status": "completed" }, "tags": [] @@ -721,16 +723,16 @@ "execution_count": 11, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:58.762626Z", - "iopub.status.busy": "2021-08-16T14:56:58.761824Z", - "iopub.status.idle": "2021-08-16T14:56:58.765299Z", - "shell.execute_reply": "2021-08-16T14:56:58.765732Z" + "iopub.execute_input": "2021-09-02T11:59:21.848897Z", + "iopub.status.busy": "2021-09-02T11:59:21.848326Z", + "iopub.status.idle": "2021-09-02T11:59:21.851330Z", + "shell.execute_reply": "2021-09-02T11:59:21.851711Z" }, "papermill": { - "duration": 0.013994, - "end_time": "2021-08-16T14:56:58.765899", + "duration": 0.013666, + "end_time": "2021-09-02T11:59:21.851883", "exception": false, - "start_time": "2021-08-16T14:56:58.751905", + "start_time": "2021-09-02T11:59:21.838217", "status": "completed" }, "tags": [] @@ -751,10 +753,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005735, - "end_time": "2021-08-16T14:56:58.777964", + "duration": 0.00606, + "end_time": "2021-09-02T11:59:21.864113", "exception": false, - "start_time": "2021-08-16T14:56:58.772229", + "start_time": "2021-09-02T11:59:21.858053", "status": "completed" }, "tags": [] @@ -770,16 +772,16 @@ "execution_count": 12, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:58.796443Z", - "iopub.status.busy": "2021-08-16T14:56:58.795852Z", - "iopub.status.idle": "2021-08-16T14:56:58.798223Z", - "shell.execute_reply": "2021-08-16T14:56:58.798592Z" + "iopub.execute_input": "2021-09-02T11:59:21.882195Z", + "iopub.status.busy": "2021-09-02T11:59:21.881652Z", + "iopub.status.idle": "2021-09-02T11:59:21.883933Z", + "shell.execute_reply": "2021-09-02T11:59:21.884457Z" }, "papermill": { - "duration": 0.015121, - "end_time": "2021-08-16T14:56:58.798843", + "duration": 0.014605, + "end_time": "2021-09-02T11:59:21.884640", "exception": false, - "start_time": "2021-08-16T14:56:58.783722", + "start_time": "2021-09-02T11:59:21.870035", "status": "completed" }, "tags": [] @@ -826,10 +828,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005883, - "end_time": "2021-08-16T14:56:58.811238", + "duration": 0.006088, + "end_time": "2021-09-02T11:59:21.897039", "exception": false, - "start_time": "2021-08-16T14:56:58.805355", + "start_time": "2021-09-02T11:59:21.890951", "status": "completed" }, "tags": [] @@ -852,16 +854,16 @@ "execution_count": 13, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:58.915074Z", - "iopub.status.busy": "2021-08-16T14:56:58.870857Z", - "iopub.status.idle": "2021-08-16T14:56:59.357262Z", - "shell.execute_reply": "2021-08-16T14:56:59.357703Z" + "iopub.execute_input": "2021-09-02T11:59:22.004097Z", + "iopub.status.busy": "2021-09-02T11:59:21.958676Z", + "iopub.status.idle": "2021-09-02T11:59:22.488171Z", + "shell.execute_reply": "2021-09-02T11:59:22.488647Z" }, "papermill": { - "duration": 0.540634, - "end_time": "2021-08-16T14:56:59.357879", + "duration": 0.585785, + "end_time": "2021-09-02T11:59:22.488865", "exception": false, - "start_time": "2021-08-16T14:56:58.817245", + "start_time": "2021-09-02T11:59:21.903080", "status": "completed" }, "tags": [] @@ -885,10 +887,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006181, - "end_time": "2021-08-16T14:56:59.370873", + "duration": 0.00634, + "end_time": "2021-09-02T11:59:22.502991", "exception": false, - "start_time": "2021-08-16T14:56:59.364692", + "start_time": "2021-09-02T11:59:22.496651", "status": "completed" }, "tags": [] @@ -902,16 +904,16 @@ "execution_count": 14, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:59.386811Z", - "iopub.status.busy": "2021-08-16T14:56:59.386162Z", - "iopub.status.idle": "2021-08-16T14:56:59.392699Z", - "shell.execute_reply": "2021-08-16T14:56:59.393078Z" + "iopub.execute_input": "2021-09-02T11:59:22.520375Z", + "iopub.status.busy": "2021-09-02T11:59:22.519727Z", + "iopub.status.idle": "2021-09-02T11:59:22.528856Z", + "shell.execute_reply": "2021-09-02T11:59:22.529563Z" }, "papermill": { - "duration": 0.016488, - "end_time": "2021-08-16T14:56:59.393248", + "duration": 0.019653, + "end_time": "2021-09-02T11:59:22.529741", "exception": false, - "start_time": "2021-08-16T14:56:59.376760", + "start_time": "2021-09-02T11:59:22.510088", "status": "completed" }, "tags": [] @@ -939,16 +941,16 @@ "execution_count": 15, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:59.409470Z", - "iopub.status.busy": "2021-08-16T14:56:59.408832Z", - "iopub.status.idle": "2021-08-16T14:56:59.410482Z", - "shell.execute_reply": "2021-08-16T14:56:59.410925Z" + "iopub.execute_input": "2021-09-02T11:59:22.546315Z", + "iopub.status.busy": "2021-09-02T11:59:22.545483Z", + "iopub.status.idle": "2021-09-02T11:59:22.547572Z", + "shell.execute_reply": "2021-09-02T11:59:22.548007Z" }, "papermill": { - "duration": 0.011631, - "end_time": "2021-08-16T14:56:59.411089", + "duration": 0.011592, + "end_time": "2021-09-02T11:59:22.548184", "exception": false, - "start_time": "2021-08-16T14:56:59.399458", + "start_time": "2021-09-02T11:59:22.536592", "status": "completed" }, "tags": [] @@ -963,16 +965,16 @@ "execution_count": 16, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:59.426921Z", - "iopub.status.busy": "2021-08-16T14:56:59.426323Z", - "iopub.status.idle": "2021-08-16T14:56:59.427920Z", - "shell.execute_reply": "2021-08-16T14:56:59.428460Z" + "iopub.execute_input": "2021-09-02T11:59:22.563956Z", + "iopub.status.busy": "2021-09-02T11:59:22.563339Z", + "iopub.status.idle": "2021-09-02T11:59:22.564833Z", + "shell.execute_reply": "2021-09-02T11:59:22.565264Z" }, "papermill": { - "duration": 0.011414, - "end_time": "2021-08-16T14:56:59.428627", + "duration": 0.011073, + "end_time": "2021-09-02T11:59:22.565436", "exception": false, - "start_time": "2021-08-16T14:56:59.417213", + "start_time": "2021-09-02T11:59:22.554363", "status": "completed" }, "tags": [] @@ -987,16 +989,16 @@ "execution_count": 17, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:59.444197Z", - "iopub.status.busy": "2021-08-16T14:56:59.443579Z", - "iopub.status.idle": "2021-08-16T14:56:59.445273Z", - "shell.execute_reply": "2021-08-16T14:56:59.445820Z" + "iopub.execute_input": "2021-09-02T11:59:22.581176Z", + "iopub.status.busy": "2021-09-02T11:59:22.580518Z", + "iopub.status.idle": "2021-09-02T11:59:22.582390Z", + "shell.execute_reply": "2021-09-02T11:59:22.582897Z" }, "papermill": { - "duration": 0.011179, - "end_time": "2021-08-16T14:56:59.446070", + "duration": 0.011518, + "end_time": "2021-09-02T11:59:22.583066", "exception": false, - "start_time": "2021-08-16T14:56:59.434891", + "start_time": "2021-09-02T11:59:22.571548", "status": "completed" }, "tags": [] @@ -1011,16 +1013,16 @@ "execution_count": 18, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:59.462442Z", - "iopub.status.busy": "2021-08-16T14:56:59.461850Z", - "iopub.status.idle": "2021-08-16T14:56:59.463926Z", - "shell.execute_reply": "2021-08-16T14:56:59.464360Z" + "iopub.execute_input": "2021-09-02T11:59:22.599580Z", + "iopub.status.busy": "2021-09-02T11:59:22.598949Z", + "iopub.status.idle": "2021-09-02T11:59:22.601161Z", + "shell.execute_reply": "2021-09-02T11:59:22.601526Z" }, "papermill": { - "duration": 0.011816, - "end_time": "2021-08-16T14:56:59.464524", + "duration": 0.012367, + "end_time": "2021-09-02T11:59:22.601691", "exception": false, - "start_time": "2021-08-16T14:56:59.452708", + "start_time": "2021-09-02T11:59:22.589324", "status": "completed" }, "tags": [] @@ -1030,7 +1032,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Run finished at 2021-08-16 16:56:59.460741\n" + "Run finished at 2021-09-02 13:59:22.597801\n" ] } ], @@ -1042,10 +1044,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006257, - "end_time": "2021-08-16T14:56:59.477403", + "duration": 0.006803, + "end_time": "2021-09-02T11:59:22.614891", "exception": false, - "start_time": "2021-08-16T14:56:59.471146", + "start_time": "2021-09-02T11:59:22.608088", "status": "completed" }, "tags": [] @@ -1059,16 +1061,16 @@ "execution_count": 19, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:59.493125Z", - "iopub.status.busy": "2021-08-16T14:56:59.492583Z", - "iopub.status.idle": "2021-08-16T14:56:59.494316Z", - "shell.execute_reply": "2021-08-16T14:56:59.494750Z" + "iopub.execute_input": "2021-09-02T11:59:22.631309Z", + "iopub.status.busy": "2021-09-02T11:59:22.630669Z", + "iopub.status.idle": "2021-09-02T11:59:22.632562Z", + "shell.execute_reply": "2021-09-02T11:59:22.632937Z" }, "papermill": { - "duration": 0.011498, - "end_time": "2021-08-16T14:56:59.494914", + "duration": 0.011952, + "end_time": "2021-09-02T11:59:22.633105", "exception": false, - "start_time": "2021-08-16T14:56:59.483416", + "start_time": "2021-09-02T11:59:22.621153", "status": "completed" }, "tags": [] @@ -1084,16 +1086,16 @@ "execution_count": 20, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:56:59.511470Z", - "iopub.status.busy": "2021-08-16T14:56:59.510914Z", - "iopub.status.idle": "2021-08-16T14:57:01.960393Z", - "shell.execute_reply": "2021-08-16T14:57:01.961059Z" + "iopub.execute_input": "2021-09-02T11:59:22.649690Z", + "iopub.status.busy": "2021-09-02T11:59:22.648973Z", + "iopub.status.idle": "2021-09-02T11:59:25.621112Z", + "shell.execute_reply": "2021-09-02T11:59:25.621787Z" }, "papermill": { - "duration": 2.459982, - "end_time": "2021-08-16T14:57:01.961254", + "duration": 2.982513, + "end_time": "2021-09-02T11:59:25.621999", "exception": false, - "start_time": "2021-08-16T14:56:59.501272", + "start_time": "2021-09-02T11:59:22.639486", "status": "completed" }, "tags": [] @@ -1105,7 +1107,7 @@ "text": [ "Watermark\n", "---------\n", - "Last updated: 2021-08-16T16:56:59.520719+02:00\n", + "Last updated: 2021-09-02T13:59:22.664670+02:00\n", "\n", "Python implementation: CPython\n", "Python version : 3.8.8\n", @@ -1119,14 +1121,14 @@ "CPU cores : 8\n", "Architecture: 64bit\n", "\n", - "Hostname: Talias-MBP.fritz.box\n", + "Hostname: Talias-MacBook-Pro.local\n", "\n", - "Git hash: 9b0bf29d81be3382d2fb1c08652fedd0cc38bd83\n", + "Git hash: 66e9d900aec806992ec40ac8180bd45f5e1b1512\n", "\n", - "awkward: 1.2.3\n", + "numpy : 1.20.2\n", "sys : 3.8.8 | packaged by conda-forge | (default, Feb 20 2021, 16:12:38) \n", "[Clang 11.0.1 ]\n", - "numpy : 1.20.2\n", + "awkward: 1.2.3\n", "\n", "Watermark: 2.2.0\n", "\n", @@ -1275,7 +1277,7 @@ "jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge\n", "jupyterlab_server 2.5.0 pyhd8ed1ab_0 conda-forge\n", "jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge\n", - "kinoml 0+untagged.632.gcb52174 dev_0 \n", + "kinoml 0+untagged.643.g6293842.dirty dev_0 \n", "kiwisolver 1.3.1 py38hd9c93a9_1 conda-forge\n", "klifs-utils 0+unknown pypi_0 pypi\n", "krb5 1.17.2 h60d9502_0 conda-forge\n", @@ -1491,16 +1493,16 @@ "execution_count": 21, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:01.984017Z", - "iopub.status.busy": "2021-08-16T14:57:01.981868Z", - "iopub.status.idle": "2021-08-16T14:57:04.364315Z", - "shell.execute_reply": "2021-08-16T14:57:04.364883Z" + "iopub.execute_input": "2021-09-02T11:59:25.645798Z", + "iopub.status.busy": "2021-09-02T11:59:25.645185Z", + "iopub.status.idle": "2021-09-02T11:59:28.169769Z", + "shell.execute_reply": "2021-09-02T11:59:28.170746Z" }, "papermill": { - "duration": 2.395624, - "end_time": "2021-08-16T14:57:04.365090", + "duration": 2.540049, + "end_time": "2021-09-02T11:59:28.170958", "exception": false, - "start_time": "2021-08-16T14:57:01.969466", + "start_time": "2021-09-02T11:59:25.630909", "status": "completed" }, "tags": [] @@ -1516,16 +1518,16 @@ "execution_count": 22, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:04.384697Z", - "iopub.status.busy": "2021-08-16T14:57:04.383979Z", - "iopub.status.idle": "2021-08-16T14:57:04.387092Z", - "shell.execute_reply": "2021-08-16T14:57:04.387485Z" + "iopub.execute_input": "2021-09-02T11:59:28.192711Z", + "iopub.status.busy": "2021-09-02T11:59:28.192015Z", + "iopub.status.idle": "2021-09-02T11:59:28.195372Z", + "shell.execute_reply": "2021-09-02T11:59:28.195808Z" }, "papermill": { - "duration": 0.014798, - "end_time": "2021-08-16T14:57:04.387660", + "duration": 0.016524, + "end_time": "2021-09-02T11:59:28.195984", "exception": false, - "start_time": "2021-08-16T14:57:04.372862", + "start_time": "2021-09-02T11:59:28.179460", "status": "completed" }, "tags": [] @@ -1544,7 +1546,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -1562,8 +1564,8 @@ }, "papermill": { "default_parameters": {}, - "duration": 11.943579, - "end_time": "2021-08-16T14:57:04.814173", + "duration": 15.446732, + "end_time": "2021-09-02T11:59:29.645292", "environment_variables": {}, "exception": null, "input_path": "features/featurize-template.ipynb", @@ -1614,13 +1616,44 @@ "idx_val": 0.1 } }, - "start_time": "2021-08-16T14:56:52.870594", + "start_time": "2021-09-02T11:59:14.198560", "version": "2.2.0" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": { - "0c5e75b19eff4698b87897f045ba40e6": { + "1975436c9c314d3496fb09426bdbcdb3": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "DescriptionStyleModel", + "state": { + "_model_module": "@jupyter-widgets/controls", + "_model_module_version": "1.5.0", + "_model_name": "DescriptionStyleModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/base", + "_view_module_version": "1.2.0", + "_view_name": "StyleView", + "description_width": "" + } + }, + "25c82f7247124fde8da154ee426375cc": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "ProgressStyleModel", + "state": { + "_model_module": "@jupyter-widgets/controls", + "_model_module_version": "1.5.0", + "_model_name": "ProgressStyleModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/base", + "_view_module_version": "1.2.0", + "_view_name": "StyleView", + "bar_color": null, + "description_width": "" + } + }, + "2d98fc5156a4432da304b667c1292861": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1672,44 +1705,7 @@ "width": null } }, - "3f279f64006d4677a7cab77ce6d9c1c2": { - "model_module": "@jupyter-widgets/controls", - "model_module_version": "1.5.0", - "model_name": "ProgressStyleModel", - "state": { - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "ProgressStyleModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/base", - "_view_module_version": "1.2.0", - "_view_name": "StyleView", - "bar_color": null, - "description_width": "" - } - }, - "5cd342b029d44d749a555a718f7f5905": { - "model_module": "@jupyter-widgets/controls", - "model_module_version": "1.5.0", - "model_name": "HTMLModel", - "state": { - "_dom_classes": [], - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "HTMLModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/controls", - "_view_module_version": "1.5.0", - "_view_name": "HTMLView", - "description": "", - "description_tooltip": null, - "layout": "IPY_MODEL_97edfdeffefe4cc79f3dc553feb7531b", - "placeholder": "​", - "style": "IPY_MODEL_ca2a82044a9e43dfb306061e44be1ce8", - "value": "100%" - } - }, - "6c2b489d8011452eade6a2667d3c5b0b": { + "53fca31f694448c5b57d9a127fc141c9": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", "model_name": "FloatProgressModel", @@ -1725,15 +1721,15 @@ "bar_style": "success", "description": "", "description_tooltip": null, - "layout": "IPY_MODEL_a67059dd5723484eb31c30e05492f6ed", + "layout": "IPY_MODEL_6e40841920d04f2993b5be8c940988b9", "max": 100.0, "min": 0.0, "orientation": "horizontal", - "style": "IPY_MODEL_3f279f64006d4677a7cab77ce6d9c1c2", + "style": "IPY_MODEL_25c82f7247124fde8da154ee426375cc", "value": 100.0 } }, - "807c106b126b49ac8c33cb8046ea7784": { + "55278e51bbba4657b736a6c8be920c4e": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", "model_name": "HBoxModel", @@ -1748,14 +1744,14 @@ "_view_name": "HBoxView", "box_style": "", "children": [ - "IPY_MODEL_5cd342b029d44d749a555a718f7f5905", - "IPY_MODEL_6c2b489d8011452eade6a2667d3c5b0b", - "IPY_MODEL_8c476081764d4a4d90410ee66a4d5176" + "IPY_MODEL_e1a28789a7164af38e78a7674dc92c5c", + "IPY_MODEL_53fca31f694448c5b57d9a127fc141c9", + "IPY_MODEL_59018d62c9e14b0b970e6f4da2ec93e2" ], - "layout": "IPY_MODEL_ad261d3eb4204548a3d7c9b1e0652fd9" + "layout": "IPY_MODEL_83595134da8f4d24ac15fb092c4afcaa" } }, - "8c476081764d4a4d90410ee66a4d5176": { + "59018d62c9e14b0b970e6f4da2ec93e2": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", "model_name": "HTMLModel", @@ -1770,13 +1766,13 @@ "_view_name": "HTMLView", "description": "", "description_tooltip": null, - "layout": "IPY_MODEL_0c5e75b19eff4698b87897f045ba40e6", + "layout": "IPY_MODEL_2d98fc5156a4432da304b667c1292861", "placeholder": "​", - "style": "IPY_MODEL_c0ade0c60d90433b98c4721778e65f1f", - "value": " 100/100 [00:00<00:00, 4190.78it/s]" + "style": "IPY_MODEL_1975436c9c314d3496fb09426bdbcdb3", + "value": " 100/100 [00:00<00:00, 4090.13it/s]" } }, - "97edfdeffefe4cc79f3dc553feb7531b": { + "6e40841920d04f2993b5be8c940988b9": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1828,7 +1824,7 @@ "width": null } }, - "a67059dd5723484eb31c30e05492f6ed": { + "83595134da8f4d24ac15fb092c4afcaa": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1880,7 +1876,7 @@ "width": null } }, - "ad261d3eb4204548a3d7c9b1e0652fd9": { + "c459d701038f4148bcdf4a00a7057733": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1932,22 +1928,28 @@ "width": null } }, - "c0ade0c60d90433b98c4721778e65f1f": { + "e1a28789a7164af38e78a7674dc92c5c": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", - "model_name": "DescriptionStyleModel", + "model_name": "HTMLModel", "state": { + "_dom_classes": [], "_model_module": "@jupyter-widgets/controls", "_model_module_version": "1.5.0", - "_model_name": "DescriptionStyleModel", + "_model_name": "HTMLModel", "_view_count": null, - "_view_module": "@jupyter-widgets/base", - "_view_module_version": "1.2.0", - "_view_name": "StyleView", - "description_width": "" + "_view_module": "@jupyter-widgets/controls", + "_view_module_version": "1.5.0", + "_view_name": "HTMLView", + "description": "", + "description_tooltip": null, + "layout": "IPY_MODEL_c459d701038f4148bcdf4a00a7057733", + "placeholder": "​", + "style": "IPY_MODEL_e78d5a61eca248638802ec6d67b7af41", + "value": "100%" } }, - "ca2a82044a9e43dfb306061e44be1ce8": { + "e78d5a61eca248638802ec6d67b7af41": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", "model_name": "DescriptionStyleModel", diff --git a/features/ligand-only-onehotsmiles-subsample/featurize.ipynb b/features/ligand-only-onehotsmiles-subsample/featurize.ipynb index d0b7112..aaf73ab 100644 --- a/features/ligand-only-onehotsmiles-subsample/featurize.ipynb +++ b/features/ligand-only-onehotsmiles-subsample/featurize.ipynb @@ -4,10 +4,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.014539, - "end_time": "2021-08-16T14:57:06.627587", + "duration": 0.013832, + "end_time": "2021-09-02T11:59:31.517784", "exception": false, - "start_time": "2021-08-16T14:57:06.613048", + "start_time": "2021-09-02T11:59:31.503952", "status": "completed" }, "tags": [] @@ -28,10 +28,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.00688, - "end_time": "2021-08-16T14:57:06.642787", + "duration": 0.006954, + "end_time": "2021-09-02T11:59:31.532812", "exception": false, - "start_time": "2021-08-16T14:57:06.635907", + "start_time": "2021-09-02T11:59:31.525858", "status": "completed" }, "tags": [] @@ -47,16 +47,16 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:06.661640Z", - "iopub.status.busy": "2021-08-16T14:57:06.661070Z", - "iopub.status.idle": "2021-08-16T14:57:06.663085Z", - "shell.execute_reply": "2021-08-16T14:57:06.664190Z" + "iopub.execute_input": "2021-09-02T11:59:31.551760Z", + "iopub.status.busy": "2021-09-02T11:59:31.551196Z", + "iopub.status.idle": "2021-09-02T11:59:31.553007Z", + "shell.execute_reply": "2021-09-02T11:59:31.553460Z" }, "papermill": { - "duration": 0.015852, - "end_time": "2021-08-16T14:57:06.664616", + "duration": 0.014798, + "end_time": "2021-09-02T11:59:31.553689", "exception": false, - "start_time": "2021-08-16T14:57:06.648764", + "start_time": "2021-09-02T11:59:31.538891", "status": "completed" }, "tags": [] @@ -72,10 +72,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006529, - "end_time": "2021-08-16T14:57:06.678805", + "duration": 0.005666, + "end_time": "2021-09-02T11:59:31.565163", "exception": false, - "start_time": "2021-08-16T14:57:06.672276", + "start_time": "2021-09-02T11:59:31.559497", "status": "completed" }, "tags": [] @@ -89,16 +89,16 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:06.697151Z", - "iopub.status.busy": "2021-08-16T14:57:06.696571Z", - "iopub.status.idle": "2021-08-16T14:57:06.698696Z", - "shell.execute_reply": "2021-08-16T14:57:06.699153Z" + "iopub.execute_input": "2021-09-02T11:59:31.580838Z", + "iopub.status.busy": "2021-09-02T11:59:31.580288Z", + "iopub.status.idle": "2021-09-02T11:59:31.582278Z", + "shell.execute_reply": "2021-09-02T11:59:31.582650Z" }, "papermill": { - "duration": 0.01395, - "end_time": "2021-08-16T14:57:06.699322", + "duration": 0.01266, + "end_time": "2021-09-02T11:59:31.582811", "exception": false, - "start_time": "2021-08-16T14:57:06.685372", + "start_time": "2021-09-02T11:59:31.570151", "status": "completed" }, "tags": [ @@ -111,6 +111,8 @@ "DATASET_CLS = \"import.path.to.DatasetProvider\"\n", "DATASET_KWARGS = {\"option\": \"value\", \"option2\": \"value2\"}\n", "\n", + "FEATURIZE_KWARGS = {}\n", + "\n", "PIPELINES = {\n", " \"someuniquekey\": [\n", " (\"import.path.to.SomeFeaturizer\", {\"option\": \"value\", \"option2\": \"value2\"}),\n", @@ -134,19 +136,19 @@ { "cell_type": "code", "execution_count": 3, - "id": "104e2337", + "id": "15fdf6f1", "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:06.715267Z", - "iopub.status.busy": "2021-08-16T14:57:06.714589Z", - "iopub.status.idle": "2021-08-16T14:57:06.716530Z", - "shell.execute_reply": "2021-08-16T14:57:06.717055Z" + "iopub.execute_input": "2021-09-02T11:59:31.597842Z", + "iopub.status.busy": "2021-09-02T11:59:31.597294Z", + "iopub.status.idle": "2021-09-02T11:59:31.599136Z", + "shell.execute_reply": "2021-09-02T11:59:31.599566Z" }, "papermill": { - "duration": 0.012109, - "end_time": "2021-08-16T14:57:06.717232", + "duration": 0.011624, + "end_time": "2021-09-02T11:59:31.599726", "exception": false, - "start_time": "2021-08-16T14:57:06.705123", + "start_time": "2021-09-02T11:59:31.588102", "status": "completed" }, "tags": [ @@ -188,10 +190,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.00533, - "end_time": "2021-08-16T14:57:06.728011", + "duration": 0.005508, + "end_time": "2021-09-02T11:59:31.610558", "exception": false, - "start_time": "2021-08-16T14:57:06.722681", + "start_time": "2021-09-02T11:59:31.605050", "status": "completed" }, "tags": [] @@ -209,16 +211,16 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:06.744366Z", - "iopub.status.busy": "2021-08-16T14:57:06.743736Z", - "iopub.status.idle": "2021-08-16T14:57:06.746965Z", - "shell.execute_reply": "2021-08-16T14:57:06.747541Z" + "iopub.execute_input": "2021-09-02T11:59:31.630837Z", + "iopub.status.busy": "2021-09-02T11:59:31.630093Z", + "iopub.status.idle": "2021-09-02T11:59:31.633975Z", + "shell.execute_reply": "2021-09-02T11:59:31.634489Z" }, "papermill": { - "duration": 0.014486, - "end_time": "2021-08-16T14:57:06.747705", + "duration": 0.018889, + "end_time": "2021-09-02T11:59:31.634705", "exception": false, - "start_time": "2021-08-16T14:57:06.733219", + "start_time": "2021-09-02T11:59:31.615816", "status": "completed" }, "tags": [] @@ -265,16 +267,16 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:06.762474Z", - "iopub.status.busy": "2021-08-16T14:57:06.761847Z", - "iopub.status.idle": "2021-08-16T14:57:06.763573Z", - "shell.execute_reply": "2021-08-16T14:57:06.764156Z" + "iopub.execute_input": "2021-09-02T11:59:31.652285Z", + "iopub.status.busy": "2021-09-02T11:59:31.651598Z", + "iopub.status.idle": "2021-09-02T11:59:31.653450Z", + "shell.execute_reply": "2021-09-02T11:59:31.653841Z" }, "papermill": { - "duration": 0.010817, - "end_time": "2021-08-16T14:57:06.764322", + "duration": 0.012191, + "end_time": "2021-09-02T11:59:31.654012", "exception": false, - "start_time": "2021-08-16T14:57:06.753505", + "start_time": "2021-09-02T11:59:31.641821", "status": "completed" }, "tags": [] @@ -289,10 +291,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005252, - "end_time": "2021-08-16T14:57:06.775193", + "duration": 0.00544, + "end_time": "2021-09-02T11:59:31.665272", "exception": false, - "start_time": "2021-08-16T14:57:06.769941", + "start_time": "2021-09-02T11:59:31.659832", "status": "completed" }, "tags": [] @@ -306,16 +308,16 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:06.790068Z", - "iopub.status.busy": "2021-08-16T14:57:06.789521Z", - "iopub.status.idle": "2021-08-16T14:57:07.478950Z", - "shell.execute_reply": "2021-08-16T14:57:07.479394Z" + "iopub.execute_input": "2021-09-02T11:59:31.680113Z", + "iopub.status.busy": "2021-09-02T11:59:31.679568Z", + "iopub.status.idle": "2021-09-02T11:59:32.361381Z", + "shell.execute_reply": "2021-09-02T11:59:32.361920Z" }, "papermill": { - "duration": 0.699246, - "end_time": "2021-08-16T14:57:07.479606", + "duration": 0.691734, + "end_time": "2021-09-02T11:59:32.362092", "exception": false, - "start_time": "2021-08-16T14:57:06.780360", + "start_time": "2021-09-02T11:59:31.670358", "status": "completed" }, "tags": [] @@ -325,7 +327,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Run started at 2021-08-16 16:57:07.474731\n" + "Run started at 2021-09-02 13:59:32.358106\n" ] } ], @@ -348,10 +350,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006641, - "end_time": "2021-08-16T14:57:07.492027", + "duration": 0.005601, + "end_time": "2021-09-02T11:59:32.373276", "exception": false, - "start_time": "2021-08-16T14:57:07.485386", + "start_time": "2021-09-02T11:59:32.367675", "status": "completed" }, "tags": [] @@ -369,16 +371,16 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:07.507214Z", - "iopub.status.busy": "2021-08-16T14:57:07.506350Z", - "iopub.status.idle": "2021-08-16T14:57:08.310627Z", - "shell.execute_reply": "2021-08-16T14:57:08.308354Z" + "iopub.execute_input": "2021-09-02T11:59:32.388067Z", + "iopub.status.busy": "2021-09-02T11:59:32.387503Z", + "iopub.status.idle": "2021-09-02T11:59:33.209235Z", + "shell.execute_reply": "2021-09-02T11:59:33.207425Z" }, "papermill": { - "duration": 0.812827, - "end_time": "2021-08-16T14:57:08.310781", + "duration": 0.830534, + "end_time": "2021-09-02T11:59:33.209402", "exception": false, - "start_time": "2021-08-16T14:57:07.497954", + "start_time": "2021-09-02T11:59:32.378868", "status": "completed" }, "tags": [] @@ -394,7 +396,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "6ff7248388524537adf0d04d38f545a1", + "model_id": "babc9b6c29c540d19ef62b81e7b8bf79", "version_major": 2, "version_minor": 0 }, @@ -426,16 +428,16 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:08.330670Z", - "iopub.status.busy": "2021-08-16T14:57:08.330125Z", - "iopub.status.idle": "2021-08-16T14:57:08.339430Z", - "shell.execute_reply": "2021-08-16T14:57:08.339956Z" + "iopub.execute_input": "2021-09-02T11:59:33.229368Z", + "iopub.status.busy": "2021-09-02T11:59:33.228827Z", + "iopub.status.idle": "2021-09-02T11:59:33.238489Z", + "shell.execute_reply": "2021-09-02T11:59:33.238929Z" }, "papermill": { - "duration": 0.023435, - "end_time": "2021-08-16T14:57:08.340122", + "duration": 0.0237, + "end_time": "2021-09-02T11:59:33.239097", "exception": false, - "start_time": "2021-08-16T14:57:08.316687", + "start_time": "2021-09-02T11:59:33.215397", "status": "completed" }, "tags": [] @@ -595,10 +597,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005891, - "end_time": "2021-08-16T14:57:08.352099", + "duration": 0.006245, + "end_time": "2021-09-02T11:59:33.251337", "exception": false, - "start_time": "2021-08-16T14:57:08.346208", + "start_time": "2021-09-02T11:59:33.245092", "status": "completed" }, "tags": [] @@ -612,16 +614,16 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:08.368700Z", - "iopub.status.busy": "2021-08-16T14:57:08.368144Z", - "iopub.status.idle": "2021-08-16T14:57:08.372352Z", - "shell.execute_reply": "2021-08-16T14:57:08.372792Z" + "iopub.execute_input": "2021-09-02T11:59:33.268030Z", + "iopub.status.busy": "2021-09-02T11:59:33.267477Z", + "iopub.status.idle": "2021-09-02T11:59:33.271602Z", + "shell.execute_reply": "2021-09-02T11:59:33.272148Z" }, "papermill": { - "duration": 0.014981, - "end_time": "2021-08-16T14:57:08.372956", + "duration": 0.01517, + "end_time": "2021-09-02T11:59:33.272333", "exception": false, - "start_time": "2021-08-16T14:57:08.357975", + "start_time": "2021-09-02T11:59:33.257163", "status": "completed" }, "tags": [] @@ -663,16 +665,16 @@ "execution_count": 10, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:08.388508Z", - "iopub.status.busy": "2021-08-16T14:57:08.387968Z", - "iopub.status.idle": "2021-08-16T14:57:12.618751Z", - "shell.execute_reply": "2021-08-16T14:57:12.619222Z" + "iopub.execute_input": "2021-09-02T11:59:33.287912Z", + "iopub.status.busy": "2021-09-02T11:59:33.287383Z", + "iopub.status.idle": "2021-09-02T11:59:37.468048Z", + "shell.execute_reply": "2021-09-02T11:59:37.468453Z" }, "papermill": { - "duration": 4.240353, - "end_time": "2021-08-16T14:57:12.619425", + "duration": 4.190164, + "end_time": "2021-09-02T11:59:37.468696", "exception": false, - "start_time": "2021-08-16T14:57:08.379072", + "start_time": "2021-09-02T11:59:33.278532", "status": "completed" }, "tags": [] @@ -687,10 +689,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.007733, - "end_time": "2021-08-16T14:57:12.634911", + "duration": 0.006767, + "end_time": "2021-09-02T11:59:37.481967", "exception": false, - "start_time": "2021-08-16T14:57:12.627178", + "start_time": "2021-09-02T11:59:37.475200", "status": "completed" }, "tags": [] @@ -703,10 +705,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.007466, - "end_time": "2021-08-16T14:57:12.649849", + "duration": 0.006231, + "end_time": "2021-09-02T11:59:37.494520", "exception": false, - "start_time": "2021-08-16T14:57:12.642383", + "start_time": "2021-09-02T11:59:37.488289", "status": "completed" }, "tags": [] @@ -720,16 +722,16 @@ "execution_count": 11, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:12.671584Z", - "iopub.status.busy": "2021-08-16T14:57:12.670431Z", - "iopub.status.idle": "2021-08-16T14:57:12.674037Z", - "shell.execute_reply": "2021-08-16T14:57:12.674580Z" + "iopub.execute_input": "2021-09-02T11:59:37.513230Z", + "iopub.status.busy": "2021-09-02T11:59:37.512451Z", + "iopub.status.idle": "2021-09-02T11:59:37.514713Z", + "shell.execute_reply": "2021-09-02T11:59:37.515112Z" }, "papermill": { - "duration": 0.017191, - "end_time": "2021-08-16T14:57:12.674822", + "duration": 0.014441, + "end_time": "2021-09-02T11:59:37.515291", "exception": false, - "start_time": "2021-08-16T14:57:12.657631", + "start_time": "2021-09-02T11:59:37.500850", "status": "completed" }, "tags": [] @@ -750,10 +752,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.008149, - "end_time": "2021-08-16T14:57:12.690788", + "duration": 0.006312, + "end_time": "2021-09-02T11:59:37.528127", "exception": false, - "start_time": "2021-08-16T14:57:12.682639", + "start_time": "2021-09-02T11:59:37.521815", "status": "completed" }, "tags": [] @@ -769,16 +771,16 @@ "execution_count": 12, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:12.715188Z", - "iopub.status.busy": "2021-08-16T14:57:12.714500Z", - "iopub.status.idle": "2021-08-16T14:57:12.717188Z", - "shell.execute_reply": "2021-08-16T14:57:12.717852Z" + "iopub.execute_input": "2021-09-02T11:59:37.547490Z", + "iopub.status.busy": "2021-09-02T11:59:37.546899Z", + "iopub.status.idle": "2021-09-02T11:59:37.549392Z", + "shell.execute_reply": "2021-09-02T11:59:37.549810Z" }, "papermill": { - "duration": 0.019199, - "end_time": "2021-08-16T14:57:12.718048", + "duration": 0.015429, + "end_time": "2021-09-02T11:59:37.550023", "exception": false, - "start_time": "2021-08-16T14:57:12.698849", + "start_time": "2021-09-02T11:59:37.534594", "status": "completed" }, "tags": [] @@ -825,10 +827,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.008222, - "end_time": "2021-08-16T14:57:12.734342", + "duration": 0.006372, + "end_time": "2021-09-02T11:59:37.562898", "exception": false, - "start_time": "2021-08-16T14:57:12.726120", + "start_time": "2021-09-02T11:59:37.556526", "status": "completed" }, "tags": [] @@ -851,16 +853,16 @@ "execution_count": 13, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:12.846072Z", - "iopub.status.busy": "2021-08-16T14:57:12.802982Z", - "iopub.status.idle": "2021-08-16T14:57:15.044704Z", - "shell.execute_reply": "2021-08-16T14:57:15.045119Z" + "iopub.execute_input": "2021-09-02T11:59:37.668714Z", + "iopub.status.busy": "2021-09-02T11:59:37.624908Z", + "iopub.status.idle": "2021-09-02T11:59:39.886184Z", + "shell.execute_reply": "2021-09-02T11:59:39.885760Z" }, "papermill": { - "duration": 2.302423, - "end_time": "2021-08-16T14:57:15.045284", + "duration": 2.317262, + "end_time": "2021-09-02T11:59:39.886341", "exception": false, - "start_time": "2021-08-16T14:57:12.742861", + "start_time": "2021-09-02T11:59:37.569079", "status": "completed" }, "tags": [] @@ -884,10 +886,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.005915, - "end_time": "2021-08-16T14:57:15.057277", + "duration": 0.006593, + "end_time": "2021-09-02T11:59:39.899981", "exception": false, - "start_time": "2021-08-16T14:57:15.051362", + "start_time": "2021-09-02T11:59:39.893388", "status": "completed" }, "tags": [] @@ -901,16 +903,16 @@ "execution_count": 14, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:15.073895Z", - "iopub.status.busy": "2021-08-16T14:57:15.073361Z", - "iopub.status.idle": "2021-08-16T14:57:15.081165Z", - "shell.execute_reply": "2021-08-16T14:57:15.081598Z" + "iopub.execute_input": "2021-09-02T11:59:39.918687Z", + "iopub.status.busy": "2021-09-02T11:59:39.917651Z", + "iopub.status.idle": "2021-09-02T11:59:39.925884Z", + "shell.execute_reply": "2021-09-02T11:59:39.926254Z" }, "papermill": { - "duration": 0.017612, - "end_time": "2021-08-16T14:57:15.081771", + "duration": 0.01995, + "end_time": "2021-09-02T11:59:39.926418", "exception": false, - "start_time": "2021-08-16T14:57:15.064159", + "start_time": "2021-09-02T11:59:39.906468", "status": "completed" }, "tags": [] @@ -938,16 +940,16 @@ "execution_count": 15, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:15.097882Z", - "iopub.status.busy": "2021-08-16T14:57:15.097288Z", - "iopub.status.idle": "2021-08-16T14:57:15.099100Z", - "shell.execute_reply": "2021-08-16T14:57:15.099510Z" + "iopub.execute_input": "2021-09-02T11:59:39.943456Z", + "iopub.status.busy": "2021-09-02T11:59:39.941869Z", + "iopub.status.idle": "2021-09-02T11:59:39.945642Z", + "shell.execute_reply": "2021-09-02T11:59:39.946025Z" }, "papermill": { - "duration": 0.011306, - "end_time": "2021-08-16T14:57:15.099734", + "duration": 0.013259, + "end_time": "2021-09-02T11:59:39.946243", "exception": false, - "start_time": "2021-08-16T14:57:15.088428", + "start_time": "2021-09-02T11:59:39.932984", "status": "completed" }, "tags": [] @@ -962,16 +964,16 @@ "execution_count": 16, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:15.115992Z", - "iopub.status.busy": "2021-08-16T14:57:15.115445Z", - "iopub.status.idle": "2021-08-16T14:57:15.117666Z", - "shell.execute_reply": "2021-08-16T14:57:15.118089Z" + "iopub.execute_input": "2021-09-02T11:59:39.961854Z", + "iopub.status.busy": "2021-09-02T11:59:39.961263Z", + "iopub.status.idle": "2021-09-02T11:59:39.962913Z", + "shell.execute_reply": "2021-09-02T11:59:39.963470Z" }, "papermill": { - "duration": 0.011834, - "end_time": "2021-08-16T14:57:15.118247", + "duration": 0.011004, + "end_time": "2021-09-02T11:59:39.963730", "exception": false, - "start_time": "2021-08-16T14:57:15.106413", + "start_time": "2021-09-02T11:59:39.952726", "status": "completed" }, "tags": [] @@ -986,16 +988,16 @@ "execution_count": 17, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:15.134069Z", - "iopub.status.busy": "2021-08-16T14:57:15.133447Z", - "iopub.status.idle": "2021-08-16T14:57:15.135448Z", - "shell.execute_reply": "2021-08-16T14:57:15.135815Z" + "iopub.execute_input": "2021-09-02T11:59:39.980243Z", + "iopub.status.busy": "2021-09-02T11:59:39.979608Z", + "iopub.status.idle": "2021-09-02T11:59:39.981140Z", + "shell.execute_reply": "2021-09-02T11:59:39.981711Z" }, "papermill": { - "duration": 0.011572, - "end_time": "2021-08-16T14:57:15.135980", + "duration": 0.011893, + "end_time": "2021-09-02T11:59:39.981873", "exception": false, - "start_time": "2021-08-16T14:57:15.124408", + "start_time": "2021-09-02T11:59:39.969980", "status": "completed" }, "tags": [] @@ -1010,16 +1012,16 @@ "execution_count": 18, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:15.152046Z", - "iopub.status.busy": "2021-08-16T14:57:15.151501Z", - "iopub.status.idle": "2021-08-16T14:57:15.153760Z", - "shell.execute_reply": "2021-08-16T14:57:15.154126Z" + "iopub.execute_input": "2021-09-02T11:59:39.998109Z", + "iopub.status.busy": "2021-09-02T11:59:39.997368Z", + "iopub.status.idle": "2021-09-02T11:59:39.999605Z", + "shell.execute_reply": "2021-09-02T11:59:40.000026Z" }, "papermill": { - "duration": 0.012069, - "end_time": "2021-08-16T14:57:15.154288", + "duration": 0.011907, + "end_time": "2021-09-02T11:59:40.000218", "exception": false, - "start_time": "2021-08-16T14:57:15.142219", + "start_time": "2021-09-02T11:59:39.988311", "status": "completed" }, "tags": [] @@ -1029,7 +1031,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Run finished at 2021-08-16 16:57:15.150392\n" + "Run finished at 2021-09-02 13:59:39.996242\n" ] } ], @@ -1041,10 +1043,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.006188, - "end_time": "2021-08-16T14:57:15.166901", + "duration": 0.007435, + "end_time": "2021-09-02T11:59:40.014252", "exception": false, - "start_time": "2021-08-16T14:57:15.160713", + "start_time": "2021-09-02T11:59:40.006817", "status": "completed" }, "tags": [] @@ -1058,16 +1060,16 @@ "execution_count": 19, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:15.183884Z", - "iopub.status.busy": "2021-08-16T14:57:15.183219Z", - "iopub.status.idle": "2021-08-16T14:57:15.185247Z", - "shell.execute_reply": "2021-08-16T14:57:15.185750Z" + "iopub.execute_input": "2021-09-02T11:59:40.031815Z", + "iopub.status.busy": "2021-09-02T11:59:40.031025Z", + "iopub.status.idle": "2021-09-02T11:59:40.033299Z", + "shell.execute_reply": "2021-09-02T11:59:40.033739Z" }, "papermill": { - "duration": 0.012707, - "end_time": "2021-08-16T14:57:15.185934", + "duration": 0.01273, + "end_time": "2021-09-02T11:59:40.033900", "exception": false, - "start_time": "2021-08-16T14:57:15.173227", + "start_time": "2021-09-02T11:59:40.021170", "status": "completed" }, "tags": [] @@ -1083,16 +1085,16 @@ "execution_count": 20, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:15.203643Z", - "iopub.status.busy": "2021-08-16T14:57:15.202978Z", - "iopub.status.idle": "2021-08-16T14:57:17.625783Z", - "shell.execute_reply": "2021-08-16T14:57:17.626217Z" + "iopub.execute_input": "2021-09-02T11:59:40.052361Z", + "iopub.status.busy": "2021-09-02T11:59:40.051523Z", + "iopub.status.idle": "2021-09-02T11:59:42.606776Z", + "shell.execute_reply": "2021-09-02T11:59:42.607441Z" }, "papermill": { - "duration": 2.433094, - "end_time": "2021-08-16T14:57:17.626394", + "duration": 2.56751, + "end_time": "2021-09-02T11:59:42.607642", "exception": false, - "start_time": "2021-08-16T14:57:15.193300", + "start_time": "2021-09-02T11:59:40.040132", "status": "completed" }, "tags": [] @@ -1104,7 +1106,7 @@ "text": [ "Watermark\n", "---------\n", - "Last updated: 2021-08-16T16:57:15.211415+02:00\n", + "Last updated: 2021-09-02T13:59:40.061622+02:00\n", "\n", "Python implementation: CPython\n", "Python version : 3.8.8\n", @@ -1118,9 +1120,9 @@ "CPU cores : 8\n", "Architecture: 64bit\n", "\n", - "Hostname: Talias-MBP.fritz.box\n", + "Hostname: Talias-MacBook-Pro.local\n", "\n", - "Git hash: 9b0bf29d81be3382d2fb1c08652fedd0cc38bd83\n", + "Git hash: 66e9d900aec806992ec40ac8180bd45f5e1b1512\n", "\n", "numpy : 1.20.2\n", "awkward: 1.2.3\n", @@ -1274,7 +1276,7 @@ "jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge\n", "jupyterlab_server 2.5.0 pyhd8ed1ab_0 conda-forge\n", "jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge\n", - "kinoml 0+untagged.632.gcb52174 dev_0 \n", + "kinoml 0+untagged.643.g6293842.dirty dev_0 \n", "kiwisolver 1.3.1 py38hd9c93a9_1 conda-forge\n", "klifs-utils 0+unknown pypi_0 pypi\n", "krb5 1.17.2 h60d9502_0 conda-forge\n", @@ -1490,16 +1492,16 @@ "execution_count": 21, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:17.649333Z", - "iopub.status.busy": "2021-08-16T14:57:17.646758Z", - "iopub.status.idle": "2021-08-16T14:57:20.071695Z", - "shell.execute_reply": "2021-08-16T14:57:20.072147Z" + "iopub.execute_input": "2021-09-02T11:59:42.630178Z", + "iopub.status.busy": "2021-09-02T11:59:42.629622Z", + "iopub.status.idle": "2021-09-02T11:59:45.105196Z", + "shell.execute_reply": "2021-09-02T11:59:45.105674Z" }, "papermill": { - "duration": 2.438604, - "end_time": "2021-08-16T14:57:20.072389", + "duration": 2.489803, + "end_time": "2021-09-02T11:59:45.105929", "exception": false, - "start_time": "2021-08-16T14:57:17.633785", + "start_time": "2021-09-02T11:59:42.616126", "status": "completed" }, "tags": [] @@ -1515,16 +1517,16 @@ "execution_count": 22, "metadata": { "execution": { - "iopub.execute_input": "2021-08-16T14:57:20.092374Z", - "iopub.status.busy": "2021-08-16T14:57:20.091718Z", - "iopub.status.idle": "2021-08-16T14:57:20.094905Z", - "shell.execute_reply": "2021-08-16T14:57:20.095429Z" + "iopub.execute_input": "2021-09-02T11:59:45.126904Z", + "iopub.status.busy": "2021-09-02T11:59:45.126203Z", + "iopub.status.idle": "2021-09-02T11:59:45.128973Z", + "shell.execute_reply": "2021-09-02T11:59:45.129521Z" }, "papermill": { - "duration": 0.015026, - "end_time": "2021-08-16T14:57:20.095608", + "duration": 0.015496, + "end_time": "2021-09-02T11:59:45.129748", "exception": false, - "start_time": "2021-08-16T14:57:20.080582", + "start_time": "2021-09-02T11:59:45.114252", "status": "completed" }, "tags": [] @@ -1543,7 +1545,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -1561,8 +1563,8 @@ }, "papermill": { "default_parameters": {}, - "duration": 15.041015, - "end_time": "2021-08-16T14:57:20.516027", + "duration": 16.296568, + "end_time": "2021-09-02T11:59:46.651814", "environment_variables": {}, "exception": null, "input_path": "features/featurize-template.ipynb", @@ -1616,28 +1618,13 @@ "idx_val": 0.1 } }, - "start_time": "2021-08-16T14:57:05.475012", + "start_time": "2021-09-02T11:59:30.355246", "version": "2.2.0" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": { - "5170cca94fea475b9f116da3eb69d293": { - "model_module": "@jupyter-widgets/controls", - "model_module_version": "1.5.0", - "model_name": "DescriptionStyleModel", - "state": { - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "DescriptionStyleModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/base", - "_view_module_version": "1.2.0", - "_view_name": "StyleView", - "description_width": "" - } - }, - "6bf1f8a0078c442db0be96eb7b868d32": { + "02953f0a75904addbcf90e5dbdae235c": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1689,29 +1676,83 @@ "width": null } }, - "6ff7248388524537adf0d04d38f545a1": { + "237e6efcc360444983126215cb409c3d": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", - "model_name": "HBoxModel", + "model_name": "HTMLModel", "state": { "_dom_classes": [], "_model_module": "@jupyter-widgets/controls", "_model_module_version": "1.5.0", - "_model_name": "HBoxModel", + "_model_name": "HTMLModel", "_view_count": null, "_view_module": "@jupyter-widgets/controls", "_view_module_version": "1.5.0", - "_view_name": "HBoxView", - "box_style": "", - "children": [ - "IPY_MODEL_7c8e296ffb504ffd95cd8c8f50fdcf24", - "IPY_MODEL_a407f0b1da4d41688d62fab565f189e3", - "IPY_MODEL_db826a3fba67486aa04f3c54278d4bfe" - ], - "layout": "IPY_MODEL_73936db805d7411baf909442aee6896a" + "_view_name": "HTMLView", + "description": "", + "description_tooltip": null, + "layout": "IPY_MODEL_a82013a4b3f346f980b3553e11e85b1a", + "placeholder": "​", + "style": "IPY_MODEL_ef373fae7c0e48029019826825be3801", + "value": " 100/100 [00:00<00:00, 4018.80it/s]" + } + }, + "61115ea099ab4307b2643c3502ef2b65": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "FloatProgressModel", + "state": { + "_dom_classes": [], + "_model_module": "@jupyter-widgets/controls", + "_model_module_version": "1.5.0", + "_model_name": "FloatProgressModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/controls", + "_view_module_version": "1.5.0", + "_view_name": "ProgressView", + "bar_style": "success", + "description": "", + "description_tooltip": null, + "layout": "IPY_MODEL_02953f0a75904addbcf90e5dbdae235c", + "max": 100.0, + "min": 0.0, + "orientation": "horizontal", + "style": "IPY_MODEL_80cb049faaff4b7e8e56dfead1e1c53b", + "value": 100.0 + } + }, + "80cb049faaff4b7e8e56dfead1e1c53b": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "ProgressStyleModel", + "state": { + "_model_module": "@jupyter-widgets/controls", + "_model_module_version": "1.5.0", + "_model_name": "ProgressStyleModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/base", + "_view_module_version": "1.2.0", + "_view_name": "StyleView", + "bar_color": null, + "description_width": "" + } + }, + "a7d01e85130c4d499aa887a7744a5b5a": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "DescriptionStyleModel", + "state": { + "_model_module": "@jupyter-widgets/controls", + "_model_module_version": "1.5.0", + "_model_name": "DescriptionStyleModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/base", + "_view_module_version": "1.2.0", + "_view_name": "StyleView", + "description_width": "" } }, - "73936db805d7411baf909442aee6896a": { + "a82013a4b3f346f980b3553e11e85b1a": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1763,7 +1804,50 @@ "width": null } }, - "7450a871c4f648308049bdce70aa066d": { + "b73fc6fe96a64b14b991bc785174ca60": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "HTMLModel", + "state": { + "_dom_classes": [], + "_model_module": "@jupyter-widgets/controls", + "_model_module_version": "1.5.0", + "_model_name": "HTMLModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/controls", + "_view_module_version": "1.5.0", + "_view_name": "HTMLView", + "description": "", + "description_tooltip": null, + "layout": "IPY_MODEL_f7273723bc9a4fe4aacfe58080b22077", + "placeholder": "​", + "style": "IPY_MODEL_a7d01e85130c4d499aa887a7744a5b5a", + "value": "100%" + } + }, + "babc9b6c29c540d19ef62b81e7b8bf79": { + "model_module": "@jupyter-widgets/controls", + "model_module_version": "1.5.0", + "model_name": "HBoxModel", + "state": { + "_dom_classes": [], + "_model_module": "@jupyter-widgets/controls", + "_model_module_version": "1.5.0", + "_model_name": "HBoxModel", + "_view_count": null, + "_view_module": "@jupyter-widgets/controls", + "_view_module_version": "1.5.0", + "_view_name": "HBoxView", + "box_style": "", + "children": [ + "IPY_MODEL_b73fc6fe96a64b14b991bc785174ca60", + "IPY_MODEL_61115ea099ab4307b2643c3502ef2b65", + "IPY_MODEL_237e6efcc360444983126215cb409c3d" + ], + "layout": "IPY_MODEL_d9e30a8aee6f47e9a529f5d56f41e22d" + } + }, + "d9e30a8aee6f47e9a529f5d56f41e22d": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1815,28 +1899,7 @@ "width": null } }, - "7c8e296ffb504ffd95cd8c8f50fdcf24": { - "model_module": "@jupyter-widgets/controls", - "model_module_version": "1.5.0", - "model_name": "HTMLModel", - "state": { - "_dom_classes": [], - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "HTMLModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/controls", - "_view_module_version": "1.5.0", - "_view_name": "HTMLView", - "description": "", - "description_tooltip": null, - "layout": "IPY_MODEL_6bf1f8a0078c442db0be96eb7b868d32", - "placeholder": "​", - "style": "IPY_MODEL_9be0f360923b41f0be06ae4a3cde5f54", - "value": "100%" - } - }, - "9be0f360923b41f0be06ae4a3cde5f54": { + "ef373fae7c0e48029019826825be3801": { "model_module": "@jupyter-widgets/controls", "model_module_version": "1.5.0", "model_name": "DescriptionStyleModel", @@ -1851,31 +1914,7 @@ "description_width": "" } }, - "a407f0b1da4d41688d62fab565f189e3": { - "model_module": "@jupyter-widgets/controls", - "model_module_version": "1.5.0", - "model_name": "FloatProgressModel", - "state": { - "_dom_classes": [], - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "FloatProgressModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/controls", - "_view_module_version": "1.5.0", - "_view_name": "ProgressView", - "bar_style": "success", - "description": "", - "description_tooltip": null, - "layout": "IPY_MODEL_c342f71ec9374b91af9c0e593e482ac5", - "max": 100.0, - "min": 0.0, - "orientation": "horizontal", - "style": "IPY_MODEL_ee34df242e27470c9d7ca2ddf0c09d84", - "value": 100.0 - } - }, - "c342f71ec9374b91af9c0e593e482ac5": { + "f7273723bc9a4fe4aacfe58080b22077": { "model_module": "@jupyter-widgets/base", "model_module_version": "1.2.0", "model_name": "LayoutModel", @@ -1926,43 +1965,6 @@ "visibility": null, "width": null } - }, - "db826a3fba67486aa04f3c54278d4bfe": { - "model_module": "@jupyter-widgets/controls", - "model_module_version": "1.5.0", - "model_name": "HTMLModel", - "state": { - "_dom_classes": [], - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "HTMLModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/controls", - "_view_module_version": "1.5.0", - "_view_name": "HTMLView", - "description": "", - "description_tooltip": null, - "layout": "IPY_MODEL_7450a871c4f648308049bdce70aa066d", - "placeholder": "​", - "style": "IPY_MODEL_5170cca94fea475b9f116da3eb69d293", - "value": " 100/100 [00:00<00:00, 4204.98it/s]" - } - }, - "ee34df242e27470c9d7ca2ddf0c09d84": { - "model_module": "@jupyter-widgets/controls", - "model_module_version": "1.5.0", - "model_name": "ProgressStyleModel", - "state": { - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "ProgressStyleModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/base", - "_view_module_version": "1.2.0", - "_view_name": "StyleView", - "bar_color": null, - "description_width": "" - } } }, "version_major": 2, From f0a4c4211d2dded12c8c2cacb8712eb2819e2310 Mon Sep 17 00:00:00 2001 From: t-kimber Date: Thu, 2 Sep 2021 14:25:02 +0200 Subject: [PATCH 3/4] test graph experiment --- tests/experiments/test_model_ligand_only.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/experiments/test_model_ligand_only.sh b/tests/experiments/test_model_ligand_only.sh index 6f0e13c..0e6220a 100644 --- a/tests/experiments/test_model_ligand_only.sh +++ b/tests/experiments/test_model_ligand_only.sh @@ -7,10 +7,10 @@ echo "Models" echo "Ligand only" echo "Running model for '001_example-ligand-only-morgan1024-subset'" -python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-morgan1024-subset.py --overwrite +# python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-morgan1024-subset.py --overwrite echo "Running model for '001_example-ligand-only-smiles-subset.py'" # python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-smiles-subset.py --overwrite -# echo "Running model for '001_example-ligand-only-graph-subset'" -# python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-graph-subset.py --overwrite \ No newline at end of file +echo "Running model for '001_example-ligand-only-graph-subset'" +python run_notebook.py experiments/torch-train-test-debug-template.ipynb experiments/001_example-ligand-only-graph-subset.py --overwrite \ No newline at end of file From 4034009f0d791ab760e12fc9fa736a71a92f7bd4 Mon Sep 17 00:00:00 2001 From: t-kimber Date: Fri, 10 Sep 2021 10:17:51 +0200 Subject: [PATCH 4/4] add EGFR subsample scripts for graph. --- ...1_example-ligand-only-graph-EGFR-subset.py | 41 +++++++++++++++++++ features/ligand-only-graph-EGFR-subsample.py | 33 +++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 experiments/001_example-ligand-only-graph-EGFR-subset.py create mode 100644 features/ligand-only-graph-EGFR-subsample.py diff --git a/experiments/001_example-ligand-only-graph-EGFR-subset.py b/experiments/001_example-ligand-only-graph-EGFR-subset.py new file mode 100644 index 0000000..1dbfe7b --- /dev/null +++ b/experiments/001_example-ligand-only-graph-EGFR-subset.py @@ -0,0 +1,41 @@ +# ---- +# This input file is designed for experiments/torch-train-test-debug-template.ipynb +# ---- + + +# DATA -- Glob paths must be relative to the root of the repository: REPO / features +PARQUET_FILES = [ + "ligand-only-graph-EGFR-subsample/_output/ligand__SmilesToLigandFeaturizer__GraphLigandFeaturizer/ChEMBLDatasetProvider/*.parquet", +] + +# Model -- specified with the full import path to the class object +MODEL_CLS = "kinoml.ml.torch_geometric_models.GraphConvolutionNeuralNetwork" +MODEL_KWARGS = {} + + +# OPTIMIZER +OPTIMIZER = "torch.optim.Adam" +OPTIMIZER_KWARGS = {"lr": 0.001, "eps": 1e-7, "betas": [0.9, 0.999]} + +# LOSS FUNCTION +LOSS = "torch.nn.MSELoss" +LOSS_KWARGS = {} + +# TRAINING +MAX_EPOCHS = 50 +VALIDATION = True +EARLY_STOPPING_KWARGS = {} + +# DATALOADER +DATALOADER_CLS = "torch_geometric.data.DataLoader" +BATCH_SIZE = 64 +TRAIN_TEST_SPLIT = 0.2 +SHUFFLE_SPLITS = True +COLLATE_FN = None + +# Plot bootstrapping +N_BOOTSTRAPS = 1 +BOOTSTRAP_SAMPLE_RATIO = 1 + +# Output +VERBOSE = False diff --git a/features/ligand-only-graph-EGFR-subsample.py b/features/ligand-only-graph-EGFR-subsample.py new file mode 100644 index 0000000..70cfd7d --- /dev/null +++ b/features/ligand-only-graph-EGFR-subsample.py @@ -0,0 +1,33 @@ +# ---- +# This input file is designed for features/featurize-template.ipynb +# ---- + +# You can only use UPPERCASE variables for the names +# Values can ONLY be strings, numbers, lists (not tuples!) or dicts + +DATASET_CLS = "kinoml.datasets.chembl.ChEMBLDatasetProvider" +DATASET_KWARGS = { + "path_or_url": "https://github.com/openkinome/kinodata/releases/download/v0.3/EGFR-activities-chembl29-sample.zip", +} + +PIPELINES = { + "ligand": [ + ["kinoml.features.ligand.SmilesToLigandFeaturizer", {}], + ["kinoml.features.ligand.GraphLigandFeaturizer", {}], + ] +} +PIPELINES_AGG = "kinoml.features.core.TupleOfArrays" +PIPELINES_AGG_KWARGS = {} + +# Use keep=False to reduce the memory usage to a minimum +# Use keep=True if you want to debug the featurization steps +FEATURIZE_KWARGS = {"keep": False} + +GROUPS = [ + [ + "kinoml.datasets.groups.CallableGrouper", + {"function": "lambda measurement: type(measurement).__name__"}, + ], # by measurement type +] + +TRAIN_TEST_VAL_KWARGS = {"idx_train": 0.8, "idx_test": 0.1, "idx_val": 0.1}