tldr-group · isaacsquires · Mar 23, 2023 · Mar 22, 2022 · Jul 11, 2022 · Feb 9, 2023
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -0,0 +1,25 @@
+name: JOSS Paper Compile
+
+on: [push]
+
+jobs:
+    paper:
+        runs-on: ubuntu-latest
+        name: Paper Draft
+        steps:
+            - name: Checkout
+              uses: actions/checkout@v3
+            - name: Build draft PDF
+              uses: openjournals/openjournals-draft-action@master
+              with:
+                  journal: joss
+                  # This should be the path to the paper within your repo.
+                  paper-path: paper.md
+            - name: Upload
+              uses: actions/upload-artifact@v1
+              with:
+                  name: paper
+                  # This is the output path where Pandoc will write the compiled
+                  # PDF. Note, this should be the same directory as the input
+                  # paper.md
+                  path: paper.pdf
diff --git a/.github/workflows/taufactor.yml b/.github/workflows/taufactor.yml
@@ -0,0 +1,37 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: TauFactor Tests
+
+on: [push, pull_request]
+
+permissions:
+    contents: read
+
+jobs:
+    build:
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Set up Python 3.8
+              uses: actions/setup-python@v3
+              with:
+                  python-version: "3.8"
+            - name: Install dependencies
+              run: |
+                  $CONDA/bin/conda env update --file tests/environment.yml --name base
+            - name: Install taufactor
+              run: |
+                  $CONDA/bin/pip install -e .
+            - name: Lint with flake8
+              run: |
+                  $CONDA/bin/conda install flake8
+                  # stop the build if there are Python syntax errors or undefined names
+                  $CONDA/bin/flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+                  # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+                  $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+            - name: Test with pytest
+              run: |
+                  $CONDA/bin/conda install pytest
+                  $CONDA/bin/python -m pytest
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -7,10 +7,10 @@ version: 2
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+    configuration: docs/conf.py
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-   version: 3.7
-   install:
-   - requirements: docs/requirements.txt
+    version: 3.8
+    install:
+        - requirements: docs/requirements.txt
diff --git a/AUTHORS.md b/AUTHORS.md
@@ -0,0 +1,11 @@
+# Authors
+
+## Team
+
+-   Sam Cooper <[email protected]>
+-   Isaac Squires <[email protected]>
+-   Steve Kench <[email protected]>
+
+## Contributors
+
+None yet. Why not be the first?
diff --git a/AUTHORS.rst b/AUTHORS.rst
diff --git a/CONTRIBUTING.rst → CONTRIBUTING.md b/CONTRIBUTING.rst → CONTRIBUTING.md
@@ -1,125 +1,120 @@
-.. highlight:: shell
-
-============
-Contributing
-============
+# Contributing
 
 Contributions are welcome, and they are greatly appreciated! Every little bit
 helps, and credit will always be given.
 
 You can contribute in many ways:
 
-Types of Contributions
-----------------------
+## Types of Contributions
 
 Report Bugs
-~~~~~~~~~~~
 
 Report bugs at https://github.com/tldr-group/taufactor/issues.
 
 If you are reporting a bug, please include:
 
-* Your operating system name and version.
-* Any details about your local setup that might be helpful in troubleshooting.
-* Detailed steps to reproduce the bug.
+-   Your operating system name and version.
+-   Any details about your local setup that might be helpful in troubleshooting.
+-   Detailed steps to reproduce the bug.
 
-Fix Bugs
-~~~~~~~~
+## Fix Bugs
 
 Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
 wanted" is open to whoever wants to implement it.
 
-Implement Features
-~~~~~~~~~~~~~~~~~~
+## Implement Features
 
 Look through the GitHub issues for features. Anything tagged with "enhancement"
 and "help wanted" is open to whoever wants to implement it.
 
-Write Documentation
-~~~~~~~~~~~~~~~~~~~
+## Write Documentation
 
 TauFactor could always use more documentation, whether as part of the
 official TauFactor docs, in docstrings, or even on the web in blog posts,
 articles, and such.
 
-Submit Feedback
-~~~~~~~~~~~~~~~
+## Submit Feedback
 
 The best way to send feedback is to file an issue at https://github.com/tldr-group/taufactor/issues.
 
 If you are proposing a feature:
 
-* Explain in detail how it would work.
-* Keep the scope as narrow as possible, to make it easier to implement.
-* Remember that this is a volunteer-driven project, and that contributions
-  are welcome :)
+-   Explain in detail how it would work.
+-   Keep the scope as narrow as possible, to make it easier to implement.
+-   Remember that this is a volunteer-driven project, and that contributions
+    are welcome :)
 
-Get Started!
-------------
+## Get Started!
 
 Ready to contribute? Here's how to set up `taufactor` for local development.
 
 1. Fork the `taufactor` repo on GitHub.
-2. Clone your fork locally::
-
-    $ git clone [email protected]:your_name_here/taufactor.git
+2. Clone your fork locally:
 
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+```
+git clone [email protected]:your_name_here/taufactor.git
+```
 
-    $ mkvirtualenv taufactor
-    $ cd taufactor/
-    $ python setup.py develop
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
 
-4. Create a branch for local development::
+```
+mkvirtualenv taufactor
+cd taufactor/
+python setup.py develop
+```
 
-    $ git checkout -b name-of-your-bugfix-or-feature
+4. Create a branch for local development:
 
-   Now you can make your changes locally.
+```
+git checkout -b name-of-your-bugfix-or-feature
+```
 
 5. When you're done making changes, check that your changes pass flake8 and the
-   tests, including testing other Python versions with tox::
+   tests, including testing other Python versions with tox:
 
-    $ flake8 taufactor tests
-    $ python setup.py test or pytest
-    $ tox
+```
+flake8 taufactor tests
+python setup.py test or pytest
+tox
+```
 
-   To get flake8 and tox, just pip install them into your virtualenv.
+    To get flake8 and tox, just pip install them into your virtualenv.
 
-6. Commit your changes and push your branch to GitHub::
+6. Commit your changes and push your branch to GitHub:
 
-    $ git add .
-    $ git commit -m "Your detailed description of your changes."
-    $ git push origin name-of-your-bugfix-or-feature
+```
+git add .
+git commit -m "Your detailed description of your changes."
+git push origin name-of-your-bugfix-or-feature
+```
 
 7. Submit a pull request through the GitHub website.
 
-Pull Request Guidelines
------------------------
+## Pull Request Guidelines
 
 Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests.
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
-   feature to the list in README.rst.
-
-Tips
-----
+   feature to the list in README.md.
 
-To run a subset of tests::
+## Tips
 
-$ pytest tests.test_taufactor
+To run a subset of tests:
 
+pytest tests.test_taufactor
 
-Deploying
----------
+## Deploying
 
 A reminder for the maintainers on how to deploy.
 Make sure all your changes are committed (including an entry in HISTORY.rst).
-Then run::
+Then run:
 
-$ bump2version patch # possible: major / minor / patch
-$ git push
-$ git push --tags
+```
+bump2version patch # possible: major / minor / patch
+git push
+git push --tags
+```
 
 Travis will then deploy to PyPI if tests pass.
diff --git a/HISTORY.md b/HISTORY.md
@@ -0,0 +1,44 @@
+# History
+
+## 1.0.0 (2023-03-23)
+
+---
+
+-   Migrated to PyTorch from CuPy
+-   New convergence criteria
+-   New documentation style
+-   CI testing
+-   Includes TauFactor paper
+
+## 0.1.4 (2022-07-11)
+
+---
+
+-   Add TauE solver
+-   Add triple phase boundary calculations
+-   Fix cuboids not converging
+-   Fix convergence messaging
+
+## 0.1.3 (2021-03-25)
+
+---
+
+-   Hotfix code in taufactor.py
+
+## 0.1.2 (2021-03-25)
+
+---
+
+-   Added multi-phase and periodic solvers and metrics calculations
+
+## 0.1.1 (2021-02-10)
+
+---
+
+-   Removed CuPy from requirements and added installation instructions to README
+
+## 0.1.0 (2021-02-08)
+
+---
+
+-   First release on PyPI.
diff --git a/HISTORY.rst b/HISTORY.rst
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021, Isaac Squires
+Copyright (c) 2023, Isaac Squires
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,8 +1,8 @@
-include AUTHORS.rst
-include CONTRIBUTING.rst
-include HISTORY.rst
+include AUTHORS.md
+include CONTRIBUTING.md
+include HISTORY.md
 include LICENSE
-include README.rst
+include README.md
 
 recursive-include tests *
 recursive-exclude * __pycache__