Add nbsphinx metadata to pre-executed notebooks. (#1226)

* Add nbsphinx metadata to pre-executed notebooks.

* Auto-formatting.

Author: delucchi-cmu

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     # This hook should always pass. It will print a message if the local version 
     # is out of date.
   - repo: https://github.com/lincc-frameworks/pre-commit-hooks
-    rev: v0.1.2
+    rev: v0.2
     hooks:
       - id: check-lincc-frameworks-template-version
         name: Check template version
@@ -41,13 +41,13 @@ repos:
         description: Verify that pyproject.toml adheres to the established schema.
     # Verify that GitHub workflows are well formed
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.34.0
+    rev: 0.36.1
     hooks:
       - id: check-github-workflows
         args: ["--verbose"]
     # Automatically sort the imports used in .py files
   - repo: https://github.com/pycqa/isort
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: isort
         name: Run isort
@@ -85,7 +85,7 @@ repos:
           ]
     # Analyze the code style and report code that doesn't adhere.
   - repo: https://github.com/psf/black
-    rev: 25.9.0
+    rev: 26.1.0
     hooks:
       - id: black-jupyter
         name: Format code using black
@@ -108,32 +108,15 @@ repos:
           [
             "--ignore-missing-imports", # Ignore imports without type hints
           ]
-    # Make sure Sphinx can build the documentation while explicitly omitting 
-    # notebooks from the docs, so users don't have to wait through the execution 
-    # of each notebook or each commit. By default, these will be checked in the 
-    # GitHub workflows.
-  - repo: local
+  - repo: https://github.com/lincc-frameworks/pre-commit-hooks
+    rev: v0.2.1
     hooks:
-      - id: sphinx-build
-        name: Build documentation with Sphinx
-        entry: sphinx-build
-        language: system
-        always_run: true
-        exclude_types: [file, symlink]
+      - id: pre-executed-nb-never-execute
+        name: Check pre-executed notebooks
+        files: ^docs/tutorials/pre_executed/.*\.ipynb$
+        verbose: true
         args:
-          [
-            "-M", # Run sphinx in make mode, so we can use -D flag later
-                  # Note: -M requires next 3 args to be builder, source, output
-            "html", # Specify builder
-            "./docs", # Source directory of documents
-            "./_readthedocs", # Output directory for rendered documents
-            "-T", # Show full trace back on exception
-            "-E", # Don't use saved env; always read all files
-            "-d", # Flag for cached environment and doctrees
-            "./docs/_build/doctrees", # Directory
-            "-D", # Flag to override settings in conf.py
-            "exclude_patterns=tutorials/*,_build", # Exclude notebooks and build dir from pre-commit
-          ]
+          ["docs/tutorials/pre_executed/",]
     # Run unit tests, verify that they pass. Note that coverage is run against
     # the ./src directory here because that is what will be committed. In the
     # github workflow script, the coverage is run against the installed package

docs/tutorials/pre_executed/crossmatching.ipynb

@@ -2242,8 +2242,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.12.9"
+  },
+  "nbsphinx": {
+   "execute": "never"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

docs/tutorials/pre_executed/custom_search.ipynb

@@ -909,8 +909,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.12.3"
+  },
+  "nbsphinx": {
+   "execute": "never"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

docs/tutorials/pre_executed/des-gaia.ipynb

@@ -6070,8 +6070,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.10.14"
+  },
+  "nbsphinx": {
+   "execute": "never"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

docs/tutorials/pre_executed/dp1-gaia-epoch-prop.ipynb

@@ -2026,8 +2026,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.13.9"
+  },
+  "nbsphinx": {
+   "execute": "never"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

docs/tutorials/pre_executed/explode_lightcurves.ipynb

@@ -761,8 +761,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
    "version": "2.7.6"
+  },
+  "nbsphinx": {
+   "execute": "never"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

docs/tutorials/pre_executed/index_table.ipynb

@@ -1678,8 +1678,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.12.3"
+  },
+  "nbsphinx": {
+   "execute": "never"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

docs/tutorials/pre_executed/join_catalogs.ipynb

@@ -466,8 +466,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.11.13"
+  },
+  "nbsphinx": {
+   "execute": "never"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}

docs/tutorials/pre_executed/manual_verification.ipynb

@@ -528,8 +528,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.11.13"
+  },
+  "nbsphinx": {
+   "execute": "never"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}

docs/tutorials/pre_executed/map_partitions.ipynb

@@ -1317,8 +1317,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.13.11"
+  },
+  "nbsphinx": {
+   "execute": "never"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}