Update Python versions and GitHub Actions configuration (#82)

* Update supported python versions, versioneer, install, GitHub Actions; format/lint

* Update Python version support and upgrade setup-python action to v5

* Fix Python version formatting in GitHub Actions workflow

* Update Python version requirements to 3.8 or higher

* try adding blas and lapack dependencies

* Replace setup-python with conda for dependency management and remove OS-specific installation steps for BLAS and LAPACK

* Add conda-forge channel to workflow and verify Python and pip installation

* Add Miniconda version and environment activation to workflow

* Enable auto-activation of the base environment in the workflow and clean up unnecessary conda info commands

* Activate the conda environment in the workflow and ensure the base environment is auto-activated

* Add default shell configuration for workflow and remove explicit conda activation

* fix stdpopsim api call in sim nb

* fix factorial api call

* Add conditional installation of gcc and clang for Ubuntu and macOS

* gxx, not gcc

* compiler env vars

* abandon conda

* fix workflow syntax

* Update macOS version in build matrix to macos-15-large

* Update macOS condition for installing blas/lapack to macos-15-large

* Replace Ubuntu and macOS blas/lapack installation steps with Homebrew setup

* Refactor Homebrew installation steps in build workflow

* abandon macos

* matrix syntax

* Remove Python 3.13 from the build matrix in GitHub Actions workflow

* black format

* Replace DeviceArray with Array in documentation examples

* Update installation instructions to include --use-pep517 flag (see #81)

* try macos again with pep517

* no macos, install blas/lapack

.github/workflows/build-and-test.yml

@@ -12,17 +12,23 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [3.7, 3.8, 3.9]
+        os: [ubuntu-latest,]
+        # os: [ubuntu-latest, macos-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: r-lib/actions/setup-pandoc@v2
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Install blas/lapack if ubuntu
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt-get install libblas-dev liblapack-dev
+
     - name: Install
       run: |
         python -m pip install --upgrade pip

.github/workflows/docs-build-and-deploy.yml

@@ -11,12 +11,16 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Checkout 🛎️
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.12'
+
+      - name: Install blas/lapack
+        run: |
+          sudo apt-get install libblas-dev liblapack-dev
 
       - name: Install
         run: |
@@ -27,7 +31,7 @@ jobs:
           make docs
 
       - name: Deploy 🚀
-        uses: JamesIves/github-pages-deploy-action@v4.2.2
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           branch: docs # The branch the action should deploy to.
           folder: docs/_build/html # The folder the action should deploy.

.github/workflows/python-publish.yml

@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies

Makefile

@@ -2,7 +2,7 @@ default:
 
 install:
 	pip install -r requirements.txt
-	pip install -e .
+	pip install --use-pep517 -e .
 
 test:
 	pytest

docs/conf.py

@@ -115,7 +115,7 @@
 
 # This is processed by Jinja2 and inserted before each notebook
 nbsphinx_prolog = r"""
-{% set docname = 'docs/' + env.doc2path(env.docname, base=None) %}
+{% set docname = 'docs/' + env.doc2path(env.docname, base=None) | string %}
 .. only:: html
     .. role:: raw-html(raw)
         :format: html

docs/install.rst

@@ -1,7 +1,7 @@
 Installation
 ############
 
-Python 3.7 or higher is required.
+Python 3.8 or higher is required.
 
 Pip
 ===
@@ -10,6 +10,8 @@ Pip
 
   pip install mushi
 
+.. note::
+  You might need the flag ``--use-pep517`` to avoid errors installing the proxTV dependency.
 
 Conda
 =====

docs/notebooks/simulation.ipynb

@@ -43,7 +43,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,9 +74,8 @@
    "source": [
     "species = stdpopsim.get_species(\"HomSap\")\n",
     "model = species.get_demographic_model(\"Zigzag_1S14\")\n",
-    "ddb = model.get_demography_debugger()\n",
     "eta_true = mushi.eta(change_points,\n",
-    "                     1 / ddb.coalescence_rate_trajectory(steps=t,\n",
+    "                     1 / model.model.debug().coalescence_rate_trajectory(steps=t,\n",
     "                                                         lineages={0: 2},\n",
     "                                                         double_step_validation=False)[0])\n",
     "\n",
@@ -235,7 +234,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -346,7 +345,7 @@
  "metadata": {
   "celltoolbar": "Slideshow",
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "mushi",
    "language": "python",
    "name": "python3"
   },
@@ -360,7 +359,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,