why is branch missing so many things?

Merge branch 'main' into 136.checkout.tests

.github/workflows/build_conda.yml

@@ -7,13 +7,18 @@ jobs:
   build:
     runs-on: ubuntu-latest
     container:
-      image: continuumio/miniconda3:latest
+      image: ghcr.io/noaa-gfdl/fre-cli:miniconda24.7.1_gcc14.2.0
     steps:
-    - name: Checkout Files
-      uses: actions/checkout@v4
-    - name: Run Docker to Build
-      run: |
-        conda config --append channels conda-forge
-        conda config --append channels noaa-gfdl
-        conda install conda-build conda-verify
-        conda build .
+      - name: Checkout Files
+        uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
+      - name: Add mkmf to PATH
+        run: |
+          echo $PWD/mkmf/bin >> $GITHUB_PATH
+      - name: Run Conda to Build
+        run: |
+          conda config --append channels conda-forge
+          conda config --append channels noaa-gfdl
+          conda install conda-build conda-verify
+          conda build .

.github/workflows/create_test_conda_env.yml

@@ -5,44 +5,63 @@ on: [push]
 jobs:
   build-linux:
     runs-on: ubuntu-latest
-
+    container:
+      image: ghcr.io/noaa-gfdl/fre-cli:miniconda24.7.1_gcc14.2.0
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: '>=3.9'
-
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-
-    - name: Create fre-cli environment
-      run: |
-        # create environment fre-cli will be installed into
-        conda env create -f environment.yml --name fre-cli
-        # try to make sure the right things are in GITHUB_PATH
-        echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
-        # install fre-cli w pip
-        $CONDA/envs/fre-cli/bin/python -m pip install --prefix $CONDA/envs/fre-cli .
-
-    - name: Run pytest in fre-cli environment
-      run: |
-        # try to make sure the right things are in GITHUB_PATH
-        echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
-        which python
-        python --version
-        $CONDA/envs/fre-cli/bin/python --version
-        # run pytest
-        pytest --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov=fre fre/
-
-    - name: Run pylint in fre-cli environment
-      run: |
-        # try to make sure the right things are in GITHUB_PATH
-        echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
-        which python
-        python --version
-        $CONDA/envs/fre-cli/bin/python --version
-        # run pytest
-        pylint fre/ || echo "pylint returned non-zero exit code. preventing workflow from dying with this echo."
+      - uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
+      - name: Create fre-cli environment
+        run: |
+          # create environment containing all dependencies
+          # the env cannot be explicitly activated in github CI/CD
+          conda env create -f environment.yml --name fre-cli
+
+          # sets CONDA to wherever it may be on the image
+          source /root/.bashrc
+
+          # add conda env's executables and mkmf to github's PATH equiv.
+          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
+          echo $PWD/mkmf/bin >> $GITHUB_PATH
+
+          # use *conda environment's pip* to install fre-cli
+          # called w/ full path to conda's python for explicitness
+          # called as a module (-m pip) for explicitness
+          $CONDA/envs/fre-cli/bin/python -m pip install --prefix $CONDA/envs/fre-cli .
+
+      - name: Run pytest in fre-cli environment
+        run: |
+          # add spack installed binaries to front of path so that
+          # conda's netcdf/hdf5 installs don't break compilation tests
+          export path_save=$PATH
+          export PATH="/opt/views/view/bin:$PATH"
+
+          # run pytest
+          pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/
+
+          # restore original path and install genbadge to generate coverage badge based on xml
+          export PATH="$path_save"
+          pip install genbadge
+          genbadge coverage -v -i coverage.xml -o docs/cov_badge.svg
+          genbadge tests -v -i pytest_results.xml -o docs/pytest_badge.svg
+
+      - name: Run pylint in fre-cli environment
+        run: |
+          # run pylint, ignored modules avoid warnings arising from code internal to those modules
+          pylint --max-args 6 -ry --ignored-modules netCDF4,cmor fre/ || echo "pylint returned non-zero exit code. preventing workflow from dying with this echo."
+
+      - name: Install Sphinx and Build Documentation
+        run: |
+          pip install sphinx renku-sphinx-theme sphinx-rtd-theme
+          pip install --upgrade sphinx-rtd-theme
+          sphinx-apidoc --output-dir docs fre/ --separate
+          sphinx-build docs build
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: build/
+          force_orphan: true

.github/workflows/publish_conda.yml

@@ -2,20 +2,25 @@ name: publish_conda
 on:
   push:
     branches:
-    - main
+      - main
 jobs:
   publish:
     runs-on: ubuntu-latest
     container:
-      image: continuumio/miniconda3:latest
+      image: ghcr.io/noaa-gfdl/fre-cli:miniconda24.7.1_gcc14.2.0
     steps:
-    - name: Checkout Files
-      uses: actions/checkout@v4
-    - name: Run Docker to Build and Upload
-      run: |
-        conda config --append channels conda-forge
-        conda config --append channels noaa-gfdl
-        conda install conda-build anaconda-client conda-verify
-        export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
-        conda config --set anaconda_upload yes
-        conda build .
+      - name: Checkout Files
+        uses: actions/checkout@v4
+        with:
+          submodules: 'recursive'
+      - name: Add mkmf to PATH
+        run: |
+          echo $PWD/mkmf/bin >> $GITHUB_PATH
+      - name: Run Conda to Build and Publish
+        run: |
+          conda config --append channels conda-forge
+          conda config --append channels noaa-gfdl
+          conda install conda-build anaconda-client conda-verify
+          export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
+          conda config --set anaconda_upload yes
+          conda build .

.gitignore

@@ -55,6 +55,13 @@ coverage.xml
 .pytest_cache/
 cover/
 
+# files pulled/created via testing
+fre/tests/test_files/cmip6-cmor-tables/
+fre/tests/test_files/outdirfre/
+fre/pp/tests/configure_yaml_out/
+fre/yamltools/tests/combine_yamls_out/
+fre/app/generate_time_averages/tests/time_avg_test_files/
+
 # Translations
 *.mo
 *.pot

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "mkmf"]
+	path = mkmf
+	url = https://github.com/NOAA-GFDL/mkmf
+[submodule "fre/gfdl_msd_schemas"]
+	path = fre/gfdl_msd_schemas
+	url = https://github.com/NOAA-GFDL/gfdl_msd_schemas

CODE_OF_CONDUCT.md

@@ -0,0 +1,29 @@
+# fre-cli Code of Conduct
+
+## Purpose
+Modeling Systems Division, and GFDL as whole, seeks to create a friendly, safe and welcoming environment for all, regardless of gender, sexual orientation, ability, ethnicity, socioeconomic status, and religion. In order to protect this collaborative environment, the following Code of Conduct sets out a series of guidelines to follow while interacting with the fre-cli repository, and its contributors. This code applies equally to mentors, mentees, and independent contributors.
+
+## Expected Behavior
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+## Unacceptable Behavior
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Addressing Grievances:
+Unacceptable behavior from any community member will not be tolerated. Anyone asked to stop unacceptable behavior is expected to comply immediately. Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by emailing [email protected] 
+
+## Attribution
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html), version 1.4, the [Citizen Code of Conduct](https://web.archive.org/web/20200330154000/http://citizencodeofconduct.org/), and the [GFDL Code of Conduct](https://www.gfdl.noaa.gov/wp-content/uploads/2022/05/GFDL_Code_of_Conduct.pdf).

CONTRIBUTING.md

@@ -1,7 +1,7 @@
 ## **For Developers**
 
 * Developers are free to use this repository's `README.md` to familiarize with the CLI and save time from having to install any dependencies, but development within a Conda environment is heavily recommended regardless
-* Gain access to the repository with `git clone [email protected]:NOAA-GFDL/fre-cli.git` or your fork's link (recommended) and an SSH RSA key
+* Gain access to the repository with `git clone --recursive [email protected]:NOAA-GFDL/fre-cli.git` or your fork's link (recommended) and an SSH RSA key
     - Once inside the repository, developers can test local changes by running a `pip install .` inside of the root directory to install the fre-cli package locally with the newest local changes on top of the installed Conda fre-cli dependencies
     - Test as a normal user would use the CLI
 * Create a GitHub issue to reflect your contribution's background and reference it with Git commits

README.md

@@ -1,14 +1,22 @@
+<!-- from https://anaconda.org/NOAA-GFDL/fre-cli/badges -->
+[![Anaconda-Server Badge](https://anaconda.org/noaa-gfdl/fre-cli/badges/version.svg)](https://anaconda.org/noaa-gfdl/fre-cli)
+[![Anaconda-Server Badge](https://anaconda.org/noaa-gfdl/fre-cli/badges/latest_release_date.svg)](https://anaconda.org/noaa-gfdl/fre-cli)
+[![Anaconda-Server Badge](https://anaconda.org/noaa-gfdl/fre-cli/badges/latest_release_relative_date.svg)](https://anaconda.org/noaa-gfdl/fre-cli)
+[![CI](https://github.com/NOAA-GFDL/fre-cli/workflows/publish_conda/badge.svg)](https://github.com/NOAA-GFDL/fre-cli/actions?query=workflow%3Apublish_conda+branch%3Amain++)
+![Coverage Badge](https://noaa-gfdl.github.io/fre-cli/_images/cov_badge.svg)
+![Pytest Badge](https://noaa-gfdl.github.io/fre-cli/_images/pytest_badge.svg)
+
 # **FRE-CLI**
 
 FMS Runtime Environment (FRE) CLI developed using Python's Click package
 
-* [Sphinx Page](https://noaa-gfdl.github.io/fre-cli/index.html)
-* [Project Outline](https://docs.google.com/document/d/19Uc01IPuuIuMtOyAvxXj9Mn6Ivc5Ql6NZ-Q6I8YowRI/edit?usp=sharing)
+* [Sphinx Documentation](https://noaa-gfdl.github.io/fre-cli/index.html)
+<!--* ... internal doc, should remove, if anything...
+[Project Outline](https://docs.google.com/document/d/19Uc01IPuuIuMtOyAvxXj9Mn6Ivc5Ql6NZ-Q6I8YowRI/edit?usp=sharing) -->
 
 ![IMG_1076](https://github.com/NOAA-GFDL/fre-cli/assets/98476720/817cabe1-6e3b-4210-9874-b13f601265d6)
 
 ## **Background**
-
 `fre-cli` is a modern, user-friendly CLI that will allow users to call FRE commands using a **_fre_** **tool** _subtool_ syntax. Leveraging Click, an easily installable Python package available via PyPI and/or Conda, `fre-cli` gives users intuitive and easy-to-understand access to many FRE tools and workflows from one packaged, centralized CLI.
 
 ![Screenshot from 2024-04-18 13-42-04](https://github.com/NOAA-GFDL/fre-cli/assets/98476720/43c028a6-4e6a-42fe-8bec-008b6758ea9b)
@@ -29,25 +37,37 @@ FMS Runtime Environment (FRE) CLI developed using Python's Click package
 
     - _Can install local changes on top via `pip`_
     - GFDL Workstation:
-        - `module load miniforge`
-        - `conda activate /nbhome/fms/conda/envs/fre-cli`
+        ```
+        module load miniforge
+        conda activate /nbhome/fms/conda/envs/fre-cli
+        ```
     - Gaea:
-        - `module load miniforge`
-        - `conda activate /ncrc/home2/Flexible.Modeling.System/conda/envs/fre-cli`
-
+        ```
+        module use /usw/conda/modulefiles
+        module load miniforge
+        conda activate /ncrc/home2/Flexible.Modeling.System/conda/envs/fre-cli
+        ```
+
 ### (Method 3) Developer - Conda Environment Building
 * If you have Conda loaded and want to create your OWN environment for development, testing, etc.:
 
     - _Can install local changes on top via `pip`_
-    - Create a new Conda environment: `conda create -n [environmentName]`
-    - Append necessary channels
-        - `conda config --append channels noaa-gfdl` 
-        - `conda config --append channels conda-forge`
-    - Run `conda install` on needed dependencies (`conda install click` will give you access to pip as well)
-        - `conda install noaa-gfdl::fre-cli` should install the [CLI package](https://anaconda.org/NOAA-GFDL/fre-cli) created from the [`meta.yaml`](https://github.com/NOAA-GFDL/fre-cli/blob/refactoring/meta.yaml)
+    - Steps:
+        ```
+        # Create new conda enironment
+        conda create -n [environmentName]
+
+        # Append necessary channels
+        conda config --append channels noaa-gfdl
+        conda config --append channels conda-forge
+
+        # Run `conda install` on needed dependencies (`conda install click` will give you access to pip as well)
+        # should install the [CLI package](https://anaconda.org/NOAA-GFDL/fre-cli) created from the [`meta.yaml`](https://github.com/NOAA-GFDL/fre-cli/blob/refactoring/meta.yaml)
+        conda install noaa-gfdl::fre-cli         
+        ```
     - All other dependencies used by the tools are installed along with this install (configured inside the meta.yaml), with the exception of local modules
     - setup.py file allows [`fre.py`](https://github.com/NOAA-GFDL/fre-cli/blob/main/fre/fre.py) to be ran with `fre` as the entry point on the command line instead of `python fre.py`
-    - For further notes on development and contributing to `fre-cli` see [`CONTRIBUTING.md`](https://github.com/NOAA-GFDL/fre-cli/blob/breakup_README/CONTRIBUTING.md)
+    - For further notes on development and contributing to `fre-cli` see [`CONTRIBUTING.md`](https://github.com/NOAA-GFDL/fre-cli/blob/main/CONTRIBUTING.md)
 
 After one of the above, one can enter commands and follow `--help` messages for guidance. A brief rundown of commands to be provided are within each tool's folder as a `README.md`
 

docs/api.rst

@@ -0,0 +1,4 @@
+=============
+API
+=============
+Auto-harvested goodness, coming soon.

docs/badges.rst

@@ -0,0 +1,7 @@
+.. this file is explicitly for the hyperlinkage in the base README.md to the badge image files
+======
+Badges
+======
+
+.. image:: cov_badge.svg
+.. image:: pytest_badge.svg

docs/conf.py

@@ -14,7 +14,7 @@
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = []
+extensions = ['sphinx.ext.autodoc']
 
 templates_path = ['_templates']
 exclude_patterns = []