DOC: execute notebooks and ensure they're tested (#603)

* DOC: execute notebooks * fix title * use geopandas dev in notebook testing * temporarily enable user guide testing on PRs * disable execution on PRs again
pysal · Jun 15, 2024 · e6b0abf · e6b0abf
1 parent 2e6e816
commit e6b0abf
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Showing 25 changed files with 12,000 additions and 5,572 deletions.
diff --git a/.github/workflows/test_user_guide.yaml b/.github/workflows/test_user_guide.yaml
@@ -3,6 +3,9 @@ name: Test User Guide execution
 on:
   push:
     branches: [main]
+  # pull_request:
+  #     branches:
+  #       - "*"
   schedule:
     - cron: "0 0 * * 1,4"
   workflow_dispatch:
@@ -27,7 +30,7 @@ jobs:
       - name: setup micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: ci/envs/312-dev.yaml
+          environment-file: ci/envs/312-latest.yaml
 
       - name: Install momepy
         run: pip install .

diff --git a/ci/envs/312-latest.yaml b/ci/envs/312-latest.yaml
@@ -30,4 +30,7 @@ dependencies:
   - geopy
   - ipywidgets
   - Iprogress
+  - pip
+  - pip:
+    - git+https://github.com/geopandas/geopandas.git
 
diff --git a/ci/envs/test_user_guide.sh b/ci/envs/test_user_guide.sh
@@ -6,15 +6,8 @@ python -m ipykernel install --user --name geo_dev
 
 mkdir docs/user_guide/output
 
-jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1000 docs/user_guide/getting_started.ipynb --output-dir docs/user_guide/output
-jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1000 docs/user_guide/elements/*.ipynb --output-dir docs/user_guide/output
-jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1000 docs/user_guide/simple/*.ipynb --output-dir docs/user_guide/output
-jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1000 docs/user_guide/combined/*.ipynb --output-dir docs/user_guide/output
-jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1000 docs/user_guide/weights/*.ipynb --output-dir docs/user_guide/output
-jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1000 docs/user_guide/graph/convert.ipynb --output-dir docs/user_guide/output
-jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1000 docs/user_guide/graph/network.ipynb --output-dir docs/user_guide/output
-jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1000 docs/user_guide/graph/coins.ipynb --output-dir docs/user_guide/output
-jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1000 docs/user_guide/preprocessing/*.ipynb --output-dir docs/user_guide/output
-jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1000 docs/examples/*.ipynb --output-dir docs/user_guide/output
+jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=-1 docs/user_guide/getting_started.ipynb --output-dir docs/user_guide/output
+jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=-1 docs/user_guide/*/*.ipynb --output-dir docs/user_guide/output
+jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=-1 docs/examples/*.ipynb --output-dir docs/user_guide/output
 
 rm -rf docs/user_guide/output
diff --git a/docs/examples/clustering.ipynb b/docs/examples/clustering.ipynb
diff --git a/docs/user_guide/combined/distribution.ipynb b/docs/user_guide/combined/distribution.ipynb
diff --git a/docs/user_guide/combined/intensity.ipynb b/docs/user_guide/combined/intensity.ipynb
diff --git a/docs/user_guide/elements/blocks.ipynb b/docs/user_guide/elements/blocks.ipynb
@@ -17,6 +17,12 @@
     "ExecuteTime": {
      "end_time": "2023-01-09T03:04:20.365731Z",
      "start_time": "2023-01-09T03:04:18.395551Z"
+    },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:40.841149Z",
+     "iopub.status.busy": "2024-06-14T21:54:40.841038Z",
+     "iopub.status.idle": "2024-06-14T21:54:42.225014Z",
+     "shell.execute_reply": "2024-06-14T21:54:42.224691Z"
     }
    },
    "outputs": [],
@@ -39,6 +45,12 @@
     "ExecuteTime": {
      "end_time": "2023-01-09T03:04:20.510711Z",
      "start_time": "2023-01-09T03:04:20.368519Z"
+    },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:42.226913Z",
+     "iopub.status.busy": "2024-06-14T21:54:42.226744Z",
+     "iopub.status.idle": "2024-06-14T21:54:42.304459Z",
+     "shell.execute_reply": "2024-06-14T21:54:42.303941Z"
     }
    },
    "outputs": [],
@@ -57,6 +69,12 @@
      "end_time": "2023-01-09T03:04:20.918189Z",
      "start_time": "2023-01-09T03:04:20.514495Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:42.306771Z",
+     "iopub.status.busy": "2024-06-14T21:54:42.306558Z",
+     "iopub.status.idle": "2024-06-14T21:54:42.750476Z",
+     "shell.execute_reply": "2024-06-14T21:54:42.750097Z"
+    },
     "tags": [
      "hide_input"
     ]
@@ -99,6 +117,12 @@
      "end_time": "2023-01-09T03:04:21.152139Z",
      "start_time": "2023-01-09T03:04:20.920399Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:42.752870Z",
+     "iopub.status.busy": "2024-06-14T21:54:42.752603Z",
+     "iopub.status.idle": "2024-06-14T21:54:42.855072Z",
+     "shell.execute_reply": "2024-06-14T21:54:42.854242Z"
+    },
     "tags": [
      "hide_output"
     ]
@@ -124,6 +148,12 @@
     "ExecuteTime": {
      "end_time": "2023-01-09T03:04:21.158661Z",
      "start_time": "2023-01-09T03:04:21.154515Z"
+    },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:42.859539Z",
+     "iopub.status.busy": "2024-06-14T21:54:42.859361Z",
+     "iopub.status.idle": "2024-06-14T21:54:42.862441Z",
+     "shell.execute_reply": "2024-06-14T21:54:42.861749Z"
     }
    },
    "outputs": [],
@@ -140,6 +170,12 @@
      "end_time": "2023-01-09T03:04:21.443993Z",
      "start_time": "2023-01-09T03:04:21.161386Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:42.864630Z",
+     "iopub.status.busy": "2024-06-14T21:54:42.864493Z",
+     "iopub.status.idle": "2024-06-14T21:54:42.947118Z",
+     "shell.execute_reply": "2024-06-14T21:54:42.946846Z"
+    },
     "tags": [
      "hide_input"
     ]
@@ -184,6 +220,12 @@
      "end_time": "2023-01-09T03:04:21.810063Z",
      "start_time": "2023-01-09T03:04:21.446368Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:42.948896Z",
+     "iopub.status.busy": "2024-06-14T21:54:42.948764Z",
+     "iopub.status.idle": "2024-06-14T21:54:43.063020Z",
+     "shell.execute_reply": "2024-06-14T21:54:43.062593Z"
+    },
     "tags": [
      "hide_input"
     ]
@@ -231,6 +273,12 @@
      "end_time": "2023-01-09T03:04:21.819738Z",
      "start_time": "2023-01-09T03:04:21.812137Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:43.065276Z",
+     "iopub.status.busy": "2024-06-14T21:54:43.065114Z",
+     "iopub.status.idle": "2024-06-14T21:54:43.067640Z",
+     "shell.execute_reply": "2024-06-14T21:54:43.067357Z"
+    },
     "tags": [
      "remove_cell"
     ]
@@ -249,6 +297,12 @@
      "end_time": "2023-01-09T03:04:22.031326Z",
      "start_time": "2023-01-09T03:04:21.822660Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:43.069210Z",
+     "iopub.status.busy": "2024-06-14T21:54:43.069099Z",
+     "iopub.status.idle": "2024-06-14T21:54:43.162924Z",
+     "shell.execute_reply": "2024-06-14T21:54:43.162591Z"
+    },
     "tags": [
      "hide_output"
     ]
@@ -268,6 +322,12 @@
      "end_time": "2023-01-09T03:04:22.308846Z",
      "start_time": "2023-01-09T03:04:22.034348Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:43.164983Z",
+     "iopub.status.busy": "2024-06-14T21:54:43.164864Z",
+     "iopub.status.idle": "2024-06-14T21:54:43.241099Z",
+     "shell.execute_reply": "2024-06-14T21:54:43.240432Z"
+    },
     "tags": [
      "hide_input"
     ]
@@ -305,6 +365,12 @@
      "end_time": "2023-01-09T03:04:22.345948Z",
      "start_time": "2023-01-09T03:04:22.314902Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:43.243038Z",
+     "iopub.status.busy": "2024-06-14T21:54:43.242919Z",
+     "iopub.status.idle": "2024-06-14T21:54:43.249242Z",
+     "shell.execute_reply": "2024-06-14T21:54:43.248962Z"
+    },
     "tags": [
      "hide_output"
     ]
@@ -324,6 +390,12 @@
      "end_time": "2023-01-09T03:04:22.718838Z",
      "start_time": "2023-01-09T03:04:22.348541Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:43.251167Z",
+     "iopub.status.busy": "2024-06-14T21:54:43.251038Z",
+     "iopub.status.idle": "2024-06-14T21:54:43.365566Z",
+     "shell.execute_reply": "2024-06-14T21:54:43.365270Z"
+    },
     "tags": [
      "hide_input"
     ]
@@ -364,6 +436,12 @@
      "end_time": "2023-01-09T03:04:22.983856Z",
      "start_time": "2023-01-09T03:04:22.721169Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:43.367367Z",
+     "iopub.status.busy": "2024-06-14T21:54:43.367234Z",
+     "iopub.status.idle": "2024-06-14T21:54:43.436406Z",
+     "shell.execute_reply": "2024-06-14T21:54:43.436158Z"
+    },
     "tags": [
      "hide_output"
     ]
@@ -383,6 +461,12 @@
      "end_time": "2023-01-09T03:04:23.248623Z",
      "start_time": "2023-01-09T03:04:22.986461Z"
     },
+    "execution": {
+     "iopub.execute_input": "2024-06-14T21:54:43.438032Z",
+     "iopub.status.busy": "2024-06-14T21:54:43.437946Z",
+     "iopub.status.idle": "2024-06-14T21:54:43.501412Z",
+     "shell.execute_reply": "2024-06-14T21:54:43.501149Z"
+    },
     "tags": [
      "hide_input"
     ]

diff --git a/docs/user_guide/elements/enclosed.ipynb b/docs/user_guide/elements/enclosed.ipynb
diff --git a/docs/user_guide/elements/links.ipynb b/docs/user_guide/elements/links.ipynb
diff --git a/docs/user_guide/elements/tessellation.ipynb b/docs/user_guide/elements/tessellation.ipynb
diff --git a/docs/user_guide/getting_started.ipynb b/docs/user_guide/getting_started.ipynb