2024 update (#56)

* reflect update in mud * cleanup + updates + linting * rtd * readme update * typo * try supporting missing tex * typo * temporarily remove 3.7 with pip * bring back in 3.7 on 0.1.1rc3 * use latest mud version
mathematicalmichael · Jan 22, 2024 · 59b6675 · 59b6675
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -2,21 +2,21 @@ name: builds
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
     paths:
       - "src/**.py"
       - "setup.py"
       - "setup.cfg"
       - ".github/workflows/build.yml"
   pull_request:
-    branches-ignore: '**docker**'
+    branches-ignore: ["**docker**"]
     paths:
       - "src/**.py"
       - "setup.py"
       - "setup.cfg"
       - ".github/workflows/build.yml"
   schedule:
-      - cron: "0 0 1 * *"
+    - cron: "0 0 1 * *"
 
 jobs:
   build:
@@ -27,12 +27,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -42,7 +42,7 @@ jobs:
           pip install --upgrade wheel setuptools setuptools_scm
 
       - name: Inspect version info
-        run: | 
+        run: |
           python setup.py --version
           git describe --dirty --tags --long --match "*[0-9]*"
 

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -4,15 +4,15 @@ on:
   release:
     types: [published, created, edited]
   push:
-    branches: '**docker**'
+    branches: ["**docker**"]
 
 jobs:
   build_image:
     name: Build Docker image from source
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
@@ -2,27 +2,27 @@ name: examples
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
     paths:
       - "**.py"
       - ".github/workflows/examples.yml"
   pull_request:
-    paths: 
+    paths:
       - "**.py"
       - ".github/workflows/examples.yml"
   schedule:
-      - cron: "0 0 1 * *"
+    - cron: "0 0 1 * *"
 
 jobs:
   pip-build:
     name: Default ${{ matrix.python-version }}
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
@@ -32,12 +32,33 @@ jobs:
       - name: Install Dependencies
         run: |
           pip install .
+          # pip install mud==0.1.1
+          pip install -U mud
 
-      - name: Test CLI
+      - name: Test CLI (no TeX)
+        continue-on-error: true
         run: |
           cd /tmp
           mud_run_all -v
-  
+
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get install -yqq \
+            texlive-base \
+            texlive-latex-base \
+            texlive-latex-extra \
+            texlive-fonts-recommended \
+            texlive-fonts-extra \
+            texlive-science \
+            latexmk \
+            dvipng \
+            cm-super
+
+      - name: Test CLI (w TeX)
+        run: |
+          cd /tmp
+          mud_run_all -v
+
       - name: Generate figures using makefile
         run: |
           cd scripts
@@ -72,7 +93,8 @@ jobs:
       - name: Install Dependencies
         run: |
           pip install .
-          pip install mud==0.1rc1
+          # pip install mud==0.1.1
+          pip install -U mud
 
       - name: Conda information
         run: conda list

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -2,37 +2,37 @@ name: tests
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
     paths:
       - "src/**.py"
       - "setup.py"
       - "setup.cfg"
       - ".github/workflows/main.yml"
   pull_request:
-    branches-ignore: "**docker**"
+    branches-ignore: ["**docker**"]
     paths:
       - "src/**.py"
       - "setup.py"
       - "setup.cfg"
       - ".github/workflows/main.yml"
   schedule:
-      - cron: "0 0 */7 * *"
+    - cron: "0 0 */7 * *"
 
 jobs:
   test:
     name: Run unit tests
     strategy:
       matrix:
-        python-version: ["3.7", "3.10"]
+        python-version: ["3.7", "3.10", "3.12"]
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -43,4 +43,3 @@ jobs:
 
       - name: Run unit tests
         run: pytest
-
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -4,7 +4,7 @@ on:
   # release: [published, created, edited]
   push:
     tags:
-      - 'v*'
+      - "v*"
 
 jobs:
   pypi:
@@ -15,12 +15,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -45,7 +45,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Login to DockerHub
         uses: docker/login-action@v1

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -4,6 +4,11 @@
 # Required
 version: 2
 
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.8"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
@@ -18,7 +23,6 @@ formats:
   - epub
 
 python:
-  version: 3.8
   install:
     - requirements: docs/requirements.txt
     - method: pip

diff --git a/README.md b/README.md
@@ -11,11 +11,31 @@
 Authors: Troy Butler & Michael Pilosov
 
 # Installation
+For Python 3.7-3.12:
 
 ```sh
 pip install mud-examples
 ```
 
+To reproduce the results in Michael's thesis, use `mud-examples==0.1`. However, this comes with `mud==0.0.28`.
+Newer versions should still produce the same figures.
+
+TeX is recommended (but not required):
+
+```
+apt-get install -yqq \
+    texlive-base \
+    texlive-latex-base \
+    texlive-latex-extra \
+    texlive-fonts-recommended \
+    texlive-fonts-extra \
+    texlive-science \
+    latexmk \
+    dvipng \
+    cm-super
+```
+
+
 # Quickstart
 
 Generate all of the figures the way they are referenced in the paper:

diff --git a/docs/conf.py b/docs/conf.py
@@ -86,8 +86,8 @@
 templates_path = ["_templates"]
 
 # The suffix of source filenames.
-#source_suffix = ".rst"
-source_suffix = ['.rst', '.md']
+# source_suffix = ".rst"
+source_suffix = [".rst", ".md"]
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
@@ -149,9 +149,9 @@
 
 # -- Options for HTML output -------------------------------------------------
 
-#html_theme = "alabaster"
+# html_theme = "alabaster"
 
-#html_theme_options = {"sidebar_width": "300px", "page_width": "1200px"}
+# html_theme_options = {"sidebar_width": "300px", "page_width": "1200px"}
 
 
 html_theme = "furo"
@@ -205,8 +205,8 @@
 
 
 html_css_files = [
-     "custom.css",
- ]
+    "custom.css",
+]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
@@ -267,7 +267,13 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-    ("index", "user_guide.tex", "mud-examples Documentation", "Mathematical Michael", "manual")
+    (
+        "index",
+        "user_guide.tex",
+        "mud-examples Documentation",
+        "Mathematical Michael",
+        "manual",
+    )
 ]
 
 # The name of an image file (relative to this directory) to place at the top of