docs: remove ipynb files from version control (#128)

* only version jupytext-managed scripts, not notebooks
* add jupytext section to developer documentation
* use flopy CLI to regenerate classes in CI

.github/workflows/ex-rtd.yml

@@ -65,10 +65,7 @@ jobs:
         working-directory: ${{env.etc-directory}}
 
       - name: Update flopy MODFLOW 6 classes
-        run: |
-          import flopy
-          flopy.mf6.utils.generate_classes(branch="develop", backup=False)
-        shell: python
+        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
 
       - name: Install MODFLOW executables release
         uses: modflowpy/install-modflow-action@v1

.github/workflows/ex-workflow.yml

@@ -37,22 +37,16 @@ jobs:
         with:
           python-version: 3.8
 
-      - name: Print python version
-        run: |
-          python --version
-
       - name: Install Python packages
         run: |
+          python --version
           python -m pip install --upgrade pip setuptools wheel
           pip install -r requirements.pip.txt
           pip install -r requirements.usgs.txt
         working-directory: ${{env.etc-directory}}
 
       - name: Update flopy MODFLOW 6 classes
-        run: |
-          import flopy
-          flopy.mf6.utils.generate_classes(branch="develop", backup=False)
-        shell: python
+        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
 
       - name: Install MODFLOW executables release
         uses: modflowpy/install-modflow-action@v1
@@ -63,8 +57,7 @@ jobs:
           repo: modflow6-nightly-build
 
       - name: Run scripts without model runs
-        run: |
-          pytest -v -n=auto --durations=0 ci_build_files.py
+        run: pytest -v -n=auto --durations=0 ci_build_files.py
         working-directory: ${{env.etc-directory}}
 
       - name: zip input files
@@ -77,8 +70,7 @@ jobs:
         uses: actions/upload-artifact@v3
         with:
           name: zip_files
-          path: |
-            ./modflow6-examples.zip
+          path: ./modflow6-examples.zip
 
   build:
     name: current-build
@@ -126,10 +118,7 @@ jobs:
         working-directory: ${{env.etc-directory}}
 
       - name: Update flopy MODFLOW 6 classes
-        run: |
-          import flopy
-          flopy.mf6.utils.generate_classes(branch="develop", backup=False)
-        shell: python
+        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
 
       - name: Install MODFLOW executables release
         uses: modflowpy/install-modflow-action@v1
@@ -140,8 +129,7 @@ jobs:
           repo: modflow6-nightly-build
 
       - name: Run scripts
-        run: |
-          pytest -v -n=auto --durations=0 --run=True ci_build_files.py
+        run: pytest -v -n=auto --durations=0 --run=True ci_build_files.py
         working-directory: ${{env.etc-directory}}
 
       - name: Run processing script
@@ -237,9 +225,7 @@ jobs:
           path: ./current/
 
       - name: List files in the artifact directory
-        run: |
-          pwd
-          ls -R ./current/
+        run: ls -R ./current/
 
       - name: create bodyFile
         run: |

.gitignore

@@ -181,3 +181,6 @@ temp
 .doc/_images/
 .notebooks/
 .nb/
+
+# only version control jupytext-managed python scripts/*.py
+notebooks/

DEVELOPER.md

@@ -14,6 +14,7 @@ This document describes how to set up an environment to use or develop the MODFL
 - [Running the examples](#running-the-examples)
   - [Using `jupyter`](#using-jupyter)
   - [Using `pytest`](#using-pytest)
+  - [Using `jupytext`](#using-jupytext)
 - [Contributing examples](#contributing-examples)
 - [Releasing the examples](#releasing-the-examples)
   - [Generate notebooks and tables](#generate-notebooks-and-tables)
@@ -83,6 +84,14 @@ To run models, use `--run True`.
 
 To run in serial instead of parallel, omit `-n auto`.
 
+### Using `jupytext`
+
+The example scripts can be converted to notebooks with `jupytext`. For instance, from the project root, to generate and execute a notebook in `notebooks/`:
+
+```shell
+jupytext --from py --to ipynb scripts/ex-gwf-twri.py -o notebooks/ex-gwf-twri.ipynb --execute
+```
+
 ## Contributing examples
 
 Adding a new example requires adding a new example script in the `scripts/` folder and adding a new LaTeX problem description in the `doc/sections/` folder. Then open a pull request from your fork of the repository.