feat: update documentation workflow with micromamba setup and add environment-docs.yml

Author: dwr-psandhu

.github/workflows/docs.yml

@@ -22,27 +22,39 @@ jobs:
     runs-on: ubuntu-latest
     defaults:
       run:
-        shell: bash
+        shell: bash -el {0}
     steps:
       - name: Checkout
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v2
         with:
-          activate-environment: docs
-          auto-update-conda: true
-          python-version: 3.11
-          channels: conda-forge,defaults
+          environment-file: environment-docs.yml
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            python=3.13
+          init-shell: bash
+          condarc: |
+            channels:
+              - conda-forge
+              - cadwr-dms
+              - nodefaults
+            channel_priority: flexible
+
+      - name: Show environment details
+        run: |
+          micromamba info
+          micromamba list
+          python --version
+          which python
+          which sphinx-build || true
 
-      - name: Install docs dependencies
+      - name: Verify docs tooling imports
         run: |
-          conda install -y sphinx nbsphinx ipykernel jupyter nbconvert pandoc sphinx-rtd-theme \
-            click networkx h5py pandas numba diskcache tabulate
-          pip install -e .
-          python -m pip list
+          python -c "import importlib, sphinx, nbsphinx; print('sphinx', sphinx.__version__); print('nbsphinx', nbsphinx.__version__); [importlib.import_module(m) for m in ['pydsm','networkx','pandas','h5py']]; print('Imports OK')"
 
       - name: Build HTML docs
         working-directory: docsrc

docsrc/conf.py

@@ -20,7 +20,8 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
 
 import pydsm
 
@@ -32,27 +33,30 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode',
-    'nbsphinx',
-    'sphinx.ext.mathjax',]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.viewcode",
+    "nbsphinx",
+    "sphinx.ext.mathjax",
+]
 
-exclude_patterns = ['_build', '**.ipynb_checkpoints']
+exclude_patterns = ["_build", "**.ipynb_checkpoints"]
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'pydsm'
-copyright = u"2019, Nicky Sandhu"
-author = u"Nicky Sandhu"
+project = "pydsm"
+copyright = "2019, Nicky Sandhu"
+author = "Nicky Sandhu"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -73,10 +77,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -87,7 +91,11 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+html_theme_options = {
+    "navigation_depth": 3,
+    "collapse_navigation": False,
+}
 
 # Theme options are theme-specific and customize the look and feel of a
 # theme further.  For a list of options available for each theme, see the
@@ -98,13 +106,13 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'pydsmdoc'
+htmlhelp_basename = "pydsmdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -113,15 +121,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -131,21 +136,15 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'pydsm.tex',
-     u'pydsm Documentation',
-     u'Nicky Sandhu', 'manual'),
+    (master_doc, "pydsm.tex", "pydsm Documentation", "Nicky Sandhu", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pydsm',
-     u'pydsm Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pydsm", "pydsm Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -154,13 +153,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'pydsm',
-     u'pydsm Documentation',
-     author,
-     'pydsm',
-     'Python utlities for DSM2',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "pydsm",
+        "pydsm Documentation",
+        author,
+        "pydsm",
+        "Python utlities for DSM2",
+        "Miscellaneous",
+    ),
 ]
-
-
-

environment-docs.yml

@@ -0,0 +1,44 @@
+name: pydsm-docs
+channels:
+  - conda-forge
+  - cadwr-dms
+  - nodefaults
+dependencies:
+  # Core runtime (mirrors environment.yml)
+  - python=3.13
+  - pip
+  - ipykernel
+  - decorator
+  - hdf5
+  - h5py
+  - numpy<2
+  - pandas
+  - xarray
+  - pyarrow
+  - geopandas
+  - networkx
+  - dask
+  - diskcache
+  - tabulate
+  # Visualization stack
+  - bokeh
+  - matplotlib
+  - holoviews
+  - geoviews
+  - hvplot
+  - datashader
+  - panel
+  # Custom packages from channel(s)
+  - pyhecdss
+  - vtools3
+  # Documentation specific additions
+  - sphinx
+  - nbsphinx
+  - sphinx-rtd-theme
+  - jupyter
+  - nbconvert
+  - pandoc
+  # Optional speed / compilation helpers (leave commented for now)
+  # - numba
+  - pip:
+      - .

environment.yml

@@ -4,7 +4,7 @@ channels:
   - cadwr-dms
   - nodefaults
 dependencies:
-  - python=3.11
+  - python=3.13
   - pip
   - ipykernel
   - decorator