ci: fix readthedocs

* add devtools as rtd dependency
* use update_version fn directly in conf.py
* use myst-parser (and remove recommonmark)
* debug docs.yml, add explanatory comment
* update copyright year from 2020 to 2023

.build_rtd_docs/conf.py

@@ -17,6 +17,7 @@
 from subprocess import Popen, PIPE
 
 sys.path.insert(0, os.path.abspath(os.path.join("..", "doc")))
+sys.path.insert(0, os.path.abspath(os.path.join("..", "distribution")))
 
 # -- determine if running on readthedocs ------------------------------------
 on_rtd = os.environ.get("READTHEDOCS") == "True"
@@ -35,18 +36,8 @@
 
 # -- Update the modflow 6 version -------------------------------------------
 print("Update the modflow6 version")
-pth = os.path.join("..", "distribution")
-args = (
-    "python",
-    "update_version.py",
-)
-# run the command
-proc = Popen(args, stdout=PIPE, stderr=PIPE, cwd=pth)
-stdout, stderr = proc.communicate()
-if stdout:
-    print(stdout.decode("utf-8"))
-if stderr:
-    print("Errors:\n{}".format(stderr.decode("utf-8")))
+from update_version import update_version
+update_version()
 
 # -- import version from doc/version.py -------------------------------------
 from version import __version__
@@ -92,7 +83,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "MODFLOW 6 Program Documentation"
-copyright = "2020, MODFLOW Development Team"
+copyright = "2023, MODFLOW Development Team"
 author = "MODFLOW Development Team"
 
 # -- Project version ---------------------------------------------------------

.build_rtd_docs/requirements.rtd.txt

@@ -6,7 +6,8 @@ nbsphinx_link
 ipython
 ipykernel
 rtds_action
-myst_parser
+myst-parser
 sphinx_rtd_theme
 pytest
-filelock
+filelock
+modflow-devtools

.doc/conf.py

@@ -49,7 +49,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "MODFLOW 6 Program Documentation"
-copyright = "2020, MODFLOW Development Team"
+copyright = "2023, MODFLOW Development Team"
 author = "MODFLOW Development Team"
 
 # -- General configuration ---------------------------------------------------
@@ -70,7 +70,7 @@
     "sphinx.ext.viewcode",
     "IPython.sphinxext.ipython_console_highlighting",  # lowercase didn't work
     "sphinx.ext.autosectionlabel",
-    "recommonmark",
+    "myst_parser",
     "sphinx_markdown_tables",
 ]
 
@@ -82,7 +82,7 @@
 # Settings for GitHub actions integration
 if on_rtd:
     extensions.append("rtds_action")
-    rtds_action_github_repo = "MODFLOW-USGS/modflow6"
+    rtds_action_github_repo = "w-bonelli/modflow6"
     rtds_action_path = "."
     rtds_action_artifact_prefix = "rtd-files-for-"
     rtds_action_github_token = os.environ.get("GITHUB_TOKEN", None)

.doc/requirements.txt

@@ -3,4 +3,4 @@ ipython
 ipykernel
 rtds_action
 sphinx_rtd_theme
-recommonmark
+myst-parser

.github/workflows/docs.yml

@@ -22,8 +22,6 @@ jobs:
         shell: bash -l {0}
     env:
       GCC_V: 12
-      working-directory: .build_rtd_docs
-      distribution-directory: distribution
 
     steps:
       - name: Checkout modflow6
@@ -52,12 +50,10 @@ jobs:
 
       - name: Install additional packages for Sphinx using pip
         working-directory: modflow6/.build_rtd_docs
-        run: |
-          pip install -r requirements.rtd.txt
+        run: pip install -r requirements.rtd.txt
 
       - name: Print python package versions
-        run: |
-          pip list
+        run: pip list
 
       - name: Install TeX Live
         run: |
@@ -66,13 +62,11 @@ jobs:
 
       - name: Install USGS LaTeX style files and Univers font
         working-directory: usgslatex/usgsLaTeX
-        run: |
-          sudo ./install.sh --all-users
+        run: sudo ./install.sh --all-users
 
       - name: Test building files from dfn's for LaTeX
         working-directory: modflow6/autotest
-        run: |
-          pytest -v build_mfio_tex.py
+        run: pytest -v build_mfio_tex.py
 
       - name: Setup GNU Fortran ${{ env.GCC_V }}
         uses: awvwgk/setup-fortran@main
@@ -103,21 +97,19 @@ jobs:
 
       - name: Run benchmarks
         working-directory: modflow6/distribution
+        run: python benchmark.py
         env:
           GITHUB_TOKEN: ${{ github.token }}
-        run: python benchmark.py
 
       - name: Run sphinx
         working-directory: modflow6/.build_rtd_docs
-        run: |
-          make html
+        run: make html
 
-      - name: Show results
+      - name: Show benchmarks
         working-directory: modflow6/distribution
-        run: |
-          cat run-time-comparison.md
+        run: cat run-time-comparison.md
 
-      - name: Upload comparison
+      - name: Upload benchmarks
         uses: actions/upload-artifact@v3
         with:
           name: run-time-comparison
@@ -128,12 +120,13 @@ jobs:
         with:
           name: rtd-files-for-${{ github.sha }}
           path: |
-            modflow6/.build_rtd_docs/
             modflow6/.build_rtd_docs/index.rst
             modflow6/.build_rtd_docs/mf6io.rst
+            # run-time-comparison is moved to _mf6run by conf.py
             modflow6/.build_rtd_docs/_mf6run/
             modflow6/.build_rtd_docs/_mf6io/
             modflow6/.build_rtd_docs/_static/
+            
 
   rtd_trigger:
     name: rtd-trigger