More Numpy 2 Compatibility changes

.github/ISSUE_TEMPLATE/bug_report_template.md

@@ -7,31 +7,37 @@ assignees: ''
 
 ---
 
-### Prerequisites
-
+## Prerequisites
 * [ ] Can you reproduce the problem in safe mode?
 * [ ] Are you running the latest version?
 * [ ] Are you reporting to the correct repository?
 * [ ] Did you perform a cursory search?
 
-For more information, see the `CONTRIBUTING` guide.
+<!--- For more information, see the `CONTRIBUTING` guide. --->
+
+## Describe the bug
+<!--- A clear and concise description of what the bug is. --->
 
-**Describe the bug.** A clear and concise description of what the bug is.  
 
+## To Reproduce
+<!--- Steps to reproduce the behavior: --->
+1. <!--- [First Step] --->
+2. <!--- [Second Step] --->
+3. <!--- [and so on...] --->
 
-**To Reproduce.** Steps to reproduce the behavior:  
-1. [First Step]
-2. [Second Step]
-3. [and so on...]
+## Expected behavior
+<!--- A clear and concise description of what you expected to happen. -->
 
-**Expected behavior.** A clear and concise description of what you expected to happen.  
 
+## Actual behavior
+<!--- A clear and concise description of what actually happens. --->
 
-**Actual behavior.** A clear and concise description of what actually happens.  
 
+## WESTPA version and platform
+<!--- Which version you're running, on what OS, and how it was built (e.g. conda, system libraries, manually installed dependencies) --->
 
-**WESTPA version and platform.** Which version you're running, on what OS, and how it was built (e.g. conda, system libraries, manually installed dependencies)  
 
+## Additional context
+<!--- Add any other context about the problem here. If necessary config files are required to reproduce the bug, attach the files here here. --->
 
-**Additional context.** Add any other context about the problem here. If necessary config files are required to reproduce the bug, attach the files here here.  
 

.github/ISSUE_TEMPLATE/feature_request_template.md

@@ -7,14 +7,19 @@ assignees: ''
 
 ---
 
-**Is your feature request related to a problem? Please describe.** A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]  
+## Is your feature request related to a problem? Please describe
+<!--- A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] ---> 
 
 
-**Describe the solution you'd like.** A clear and concise description of what you want to happen.  
+## Describe the solution you'd like
+<!--- A clear and concise description of what you want to happen. ---> 
 
 
-**Describe alternatives you've considered.** A clear and concise description of any alternative solutions or features you've considered.  
+## Describe alternatives you've considered
+<!--- A clear and concise description of any alternative solutions or features you've considered. --->
 
 
-**Additional context.** Add any other context or screenshots about the feature request here.  
+## Additional context
+<!--- Add any other context or screenshots about the feature request here. --->
+
 

.github/pull_request_template.md

@@ -1,16 +1,21 @@
-**Issue Number.** Is this pull request related to any outstanding issues? If so, list the issue number.  
+## Issue Number
+<!--- Is this pull request related to any outstanding issues? If so, list the issue number. --->
 
 
-**Describe the changes made.** A clear and concise description of what the problem is and what you did to fix it. E.g. [...] was happening and I've changed [...] to fix it.  
+## Describe the changes made
+<!--- A clear and concise description of what the problem is and what you did to fix it. E.g. [...] was happening and I've changed [...] to fix it. -->
 
 
-**Goals and Outstanding Issues.** A clear and concise list of goals (to be) accomplished.  
+## Goals and Outstanding Issues
+<!--- A clear and concise list of goals (to be) accomplished. --->
 - [ ] 
 
-**Major files changed.**  
+## Major files changed
+<!--- Manually list files or include a diff link in the form of: https://github.com/user/westpa/compare/<initial SHA>..<final SHA> --->
 - [ ]
 
-**Status.**
+## Status
+<!--- Delete bullet points that are not relevant. --->
 - [ ] Bug fix (non-breaking change which fixes an issue)
 - [ ] New feature (non-breaking change which adds functionality)
 - [ ] Breaking change (fix or feature that would cause existing functionality to change)
@@ -21,5 +26,7 @@
 - [ ] I have added tests to cover my changes.
 - [ ] All new and existing tests passed.
 
-**Additional context.** Add any other context or screenshots about the pull request here.  
+## Additional context
+<!--- Add any other context or screenshots about the pull request here. --->
+
 

.github/workflows/build.yaml

@@ -23,20 +23,25 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [8, 9, 10, 11] # sub-versions of Python
-
+        os: ["ubuntu-latest", "macos-13", "macos-latest"]  # macos-13 is x86_64, macos-latest is arm64
+        python-version: [9, 10, 11, 12] # sub-versions of Python
+        exclude:
+          - os: macos-14
+            python-version: 8
     steps:
       - uses: actions/checkout@v4
 
+      - name: "Install HDF5 with brew"
+        if: ${{ matrix.os == 'macos-latest' }}
+        run: "brew install hdf5"
+
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.2
+        uses: pypa/cibuildwheel@v2.19.2
         env:
           CIBW_SKIP: "pp* *-musllinux*"
           CIBW_BUILD: "cp3${{ matrix.python-version }}-*"
-          CIBW_ARCHS_MACOS: "auto64" # x86_64 only
+          CIBW_ARCHS_MACOS: "auto64" # x86_64 and arm64, depending on the os
           CIBW_ARCHS_LINUX: "auto64" # x86_64 only
-          CIBW_TEST_SKIP: "*-macosx_arm64"
           CIBW_DEPENDENCY_VERSIONS: "latest"
           CIBW_TEST_COMMAND: > 
             python -c "import westpa; print(westpa.__version__)" && 
@@ -56,52 +61,11 @@ jobs:
           output-dir: wheelhouse
           config-file: "{package}/pyproject.toml"
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: artifact-wheels-${{ matrix.os }}-${{ matrix.python-version }}
           path: ./wheelhouse/*.whl
-
-#   # Split off macos arm64 building...
-#   # Disabled for now... as of 2022-10-12
-#   # Currently creates broken arm64 wheels due to dependencies; unable to check
-#   # because macos_arm64 tests are not supported in macos_x86-64
-#   build_wheels_macos_arm64:
-#     name: Build py3.${{ matrix.python-version }} wheels on Apple Silicon
-#     runs-on: ${{ matrix.os }}
-#     strategy:
-#       matrix:
-#         os: [macos-latest]
-#         python-version: [8, 9, 10, 11] # sub-versions of Python, there is no py3.7-macosx_arm64
-# 
-#     steps:
-#       - uses: actions/checkout@v4
-# 
-#       - name: Build wheels
-#         uses: pypa/cibuildwheel@v2.16.1
-#         env:
-#           CIBW_SKIP: "pp*"
-#           CIBW_BUILD: "cp3${{ matrix.python-version }}-*"
-#           CIBW_ARCHS_MACOS: "arm64"
-#           CIBW_TEST_COMMAND: > 
-#             python -c "import westpa; print(westpa.__version__)" && 
-#             python -c "import westpa.core.propagators" &&
-#             python -c "import westpa.core.binning" &&
-#             python -c "import westpa.core.kinetics" &&
-#             python -c "import westpa.core.reweight" &&
-#             python -c "import westpa.work_managers" &&
-#             python -c "import westpa.tools" &&
-#             python -c "import westpa.fasthist" &&
-#             python -c "import westpa.mclib" &&
-#             echo "All done with the import tests!"
-#             # Currently blocked by https://github.com/westpa/westpa/issues/70
-#             # python -c "import westpa.trajtree"
-#         with:
-#           package-dir: .
-#           output-dir: wheelhouse
-#           config-file: "{package}/pyproject.toml"
-# 
-#       - uses: actions/upload-artifact@v3
-#         with:
-#           path: ./wheelhouse/*.whl
+          overwrite: true
 
   build_sdist:
     name: Build source distribution
@@ -111,7 +75,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Build sdist
         run: pipx run build --sdist
@@ -131,13 +95,15 @@ jobs:
           echo "All done with the import tests!"
           # Currently blocked by https://github.com/westpa/westpa/issues/70
           # python -c "import westpa.trajtree"
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: artifact-sdist
           path: dist/*.tar.gz
+          overwrite: true
 
   upload_testpypi:
     name: test.pypi
-    needs: [build_wheels, build_sdist] #, build_wheels_macos_arm64] # Skipping the apple silicon versions...
+    needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     environment:
       name: test.pypi
@@ -151,20 +117,21 @@ jobs:
       github.repository == 'westpa/westpa' &&
       (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v'))
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           # unpacks default artifact into dist/
           # if `name: artifact` is omitted, the action will create extra parent dir
-          name: artifact
+          pattern: artifact-*
           path: dist
+          merge-multiple: true
 
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           repository_url: https://test.pypi.org/legacy/
 
   upload_pypi:
     name: PyPI
-    needs: [build_wheels, build_sdist] #, build_wheels_macos_arm64] # Skipping the apple silicon versions...
+    needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     environment:
       name: pypi
@@ -178,12 +145,13 @@ jobs:
       github.repository == 'westpa/westpa' &&
       (github.event_name == 'release' && github.event.action == 'published')
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           # unpacks default artifact into dist/
           # if `name: artifact` is omitted, the action will create extra parent dir
-          name: artifact
+          pattern: artifact-*
           path: dist
+          merge-multiple: true
 
       - uses: pypa/gh-action-pypi-publish@release/v1
           # To test: 

.github/workflows/test.yaml

@@ -20,10 +20,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: Linting
         run: |
           pip install pre-commit
@@ -34,8 +34,8 @@ jobs:
     runs-on: "${{ matrix.os }}"
     strategy:
       matrix:
-        os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        os: ["ubuntu-latest", "macos-13", "macos-latest"]  # macos-13 is x86-64, macos-latest is arm64
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -76,17 +76,19 @@ jobs:
         pytest -v --cov=westpa --cov-report=xml --color=yes tests
 
     - name: CodeCov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
         flags: unittests
         name: codecov-{{ '${{ matrix.os }}' }}-py{{ '${{ matrix.python-version }}' }}
         fail_ci_if_error: false
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   install-dev:
     strategy:
       matrix:
-        os: ["ubuntu-latest", "macos-latest"]
+        os: ["ubuntu-latest", "macos-13", "macos-latest"]  # macos-13 is x86-64, macos-latest is arm64
 
     name: "Verify dev env"
     runs-on: "${{ matrix.os }}"
@@ -95,8 +97,12 @@ jobs:
       - uses: "actions/checkout@v4"
       - uses: "actions/setup-python@v5"
         with:
-          python-version: "3.11"
+          python-version: "3.12"
+      - name: "Install HDF5 with brew if macos-arm64"
+        if: ${{ matrix.os == 'macos-latest' }}
+        run: "brew install hdf5"
       - name: "Install in dev mode"
         run: "python -m pip install -e .[dev]"
       - name: "Import package"
         run: "python -c 'import westpa; print(westpa.__version__)'"
+

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: end-of-file-fixer
         types: [python]
     -   id: trailing-whitespace
         types: [python]
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.12.1
+    rev: 24.8.0
     hooks:
       - id: black
         language_version: python3
@@ -19,7 +19,7 @@ repos:
               | doc
           )
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.1.1
     hooks:
     -   id: flake8
         exclude: > 

README.rst

@@ -78,8 +78,8 @@ WESTPA is developed and tested on Unix-like operating systems, including Linux a
 
 Regardless of the chosen method of installation, before installing WESTPA, we recommend you to first install the Python 3 version provided by the latest free `Anaconda Python distribution`_. After installing Anaconda, create a new python environment for the WESTPA install with the following::
 
-    conda create -n westpa-2.0 python=3.9
-    conda activate westpa-2.0
+    conda create -n westpa python=3.11
+    conda activate westpa
 
 Then, we recommend installing WESTPA through conda or pip. Execute either of the following::
 
@@ -94,13 +94,13 @@ See the install instructions on our `wiki`_ for more detailed information.
 
 To install from source (**not recommended**), start by downloading the corresponding tar.gz file from the `releases page`_. After downloading the file, unpack the file and install WESTPA by executing the following::
 
-    tar xvzf westpa-main.tar.gz
+    tar xvzf westpa-2022.09.tar.gz
     cd westpa
     python -m pip install -e .
 
 .. _`releases page`: https://github.com/westpa/westpa/releases
-.. _`Anaconda Python distribution`: https://www.anaconda.com/products/individual
-.. _`wiki`: https://github.com/westpa/westpa/wiki/WESTPA-Quick-Install
+.. _`Anaconda Python distribution`: https://www.anaconda.com/download
+.. _`wiki`: https://github.com/westpa/westpa/wiki/Installing-WESTPA
 
 ---------------
 Getting started