Merge pull request #42 from yoctoyotta1024/docs

update to docs
yoctoyotta1024 · Apr 15, 2024 · 52896a0 · 52896a0
2 parents 9a2ade4 + 26cf220
commit 52896a0
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -12,8 +12,8 @@ jobs:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          activate-environment: myenv
-          environment-file: environment.yml
+          activate-environment: cienv
+          environment-file: ci_environment.yaml
           auto-activate-base: false
       - run: |
           conda info
@@ -22,18 +22,18 @@ jobs:
         run: |
           conda init
           source /home/runner/.bashrc
-          conda activate /usr/share/miniconda/envs/myenv
+          conda activate /usr/share/miniconda/envs/cienv
           conda info --envs
       - name: Install Doxygen
-        run: /usr/share/miniconda/envs/myenv/bin/doxygen --version
+        run: /usr/share/miniconda/envs/cienv/bin/doxygen --version
         shell: bash
       - name: Test with pytest
         run: pytest .
       - name: Generate Doxygen Documentation
         run: cd docs &&
           mkdir build &&
           mkdir build/doxygen &&
-          /usr/share/miniconda/envs/myenv/bin/doxygen doxygen/doxygen.dox
+          /usr/share/miniconda/envs/cienv/bin/doxygen doxygen/doxygen.dox
         shell: bash
       - name: Build docs
         run: |
@@ -57,7 +57,7 @@ jobs:
         with:
           name: html-docs
           path: docs/build/html/
-      - name: Publish docs on github pages
+      - name: Publish docs on GitHub pages
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -8,6 +8,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
+    -   id: no-commit-to-branch
 -   repo: https://gitlab.com/daverona/pre-commit/cpp
     rev: 0.8.0
     hooks:

diff --git a/ci_environment.yaml b/ci_environment.yaml
@@ -0,0 +1,16 @@
+name: cienv
+dependencies:
+    - python>=3.9
+    - pytest
+    - sphinx
+    - conda-forge::doxygen>=1.10.0
+    - pip
+    - pip:
+      - numpy
+      - pytest
+      - sphinx
+      - furo
+      - sphinx_copybutton
+      - sphinxcontrib-bibtex
+      - breathe
+      - pre-commit
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -42,6 +42,7 @@ Time to get involved! Start by :doc:`installing CLEO<usage/installation>` and ex
    usage/ourdocs
 
    GitHub Repo <https://github.com/yoctoyotta1024/CLEO.git>
+   usage/good_coding
    usage/contact
    references
 

diff --git a/docs/source/intro/intro.rst b/docs/source/intro/intro.rst
@@ -47,7 +47,7 @@ Kokkos Thread Parallelism
 For performance portable thread parallelism we embrace Kokkos. As a consequence,
 Kokkos' macros and functions are littered throughout our code and many of our key data structures,
 for example Gridboxes and super-droplets, are contained within Kokkos Views. For those seeking
-advanced understanding, we defer to Kokkos' github repositories and documentation therein.
+advanced understanding, we defer to Kokkos' GitHub repositories and documentation therein.
 
 Timestepping
 ------------

diff --git a/docs/source/intro/kokkos.rst b/docs/source/intro/kokkos.rst
@@ -6,4 +6,4 @@ Kokkos! :cite:`kokkos1` :cite:`kokkos2`, :cite:`kokkos3`.
 
 It has great documentation, lectures, tutorials and more, all of which
 you can enjoy when you explore
-`Kokkos' github repositories <https://github.com/kokkos>`_.
+`Kokkos' GitHub repositories <https://github.com/kokkos>`_.
diff --git a/docs/source/usage/contributing.rst b/docs/source/usage/contributing.rst
@@ -3,11 +3,11 @@ Contributing
 
 Yes please!
 
-CLEO is a completely open source code and entirely
-open development. If you have ideas or would like to collaborate,
-simply :ref:`contact us<contact>`!
+CLEO is a completely open source code and entirely open development. If you have ideas or would
+like to collaborate, simply :ref:`contact us<contact>`!
 
-We welcome your interest and are enthusiastic about both CLEO's
-computational development and its use for scientific research.
+We welcome your interest and are enthusiastic about both CLEO's computational development and its
+use for scientific research.
 
-TODO(CB) update with commit and code formating requirements
+Please see our documentation about :doc:`good coding practices <good_coding>` to ensure your
+contributions comply with our standards.