Merge branch 'develop' of ssh://github.com/westpa/westpa into cleanup

.github/workflows/build.yaml

@@ -24,10 +24,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-13", "macos-latest"]  # macos-13 is x86_64, macos-latest is arm64
-        python-version: [8, 9, 10, 11, 12] # sub-versions of Python
-        exclude:
-          - os: macos-14
-            python-version: 8
+        python-version: [9, 10, 11, 12] # sub-versions of Python
     steps:
       - uses: actions/checkout@v4
 
@@ -36,7 +33,7 @@ jobs:
         run: "brew install hdf5"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.20.0
+        uses: pypa/cibuildwheel@v2.21.3
         env:
           CIBW_SKIP: "pp* *-musllinux*"
           CIBW_BUILD: "cp3${{ matrix.python-version }}-*"
@@ -156,3 +153,21 @@ jobs:
       - uses: pypa/gh-action-pypi-publish@release/v1
           # To test: 
           #repository_url: https://test.pypi.org/legacy/
+
+  update-tags:
+    name: Update develop branch tags
+    needs: [upload_pypi]
+    runs-on: ubuntu-latest
+    # Assuming that since it has sucessfully uploaded to PyPI, this release is safe.
+    # We will now automatically update the tags for develop.
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: pulling tags
+        run: |
+          git checkout develop
+          git pull --tags origin westpa2
+          git push origin develop --tags
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/mirror.yaml

@@ -0,0 +1,22 @@
+name: Mirror develop to westpa2
+
+on:
+  schedule:
+    # Once a month on the 28th day at 4 pm UTC, which is ~11 am EST.
+    - cron: "00 16 28 * *"
+
+jobs:
+  mirror-develop-to-westpa2:
+    runs-on: ubuntu-latest
+    name: Mirror develop branch to westpa2 branch
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: mirroring step
+        run: |
+          git checkout westpa2
+          git pull --ff-only origin develop
+          git push origin westpa2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test.yaml

@@ -35,7 +35,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-13", "macos-latest"]  # macos-13 is x86-64, macos-latest is arm64
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -53,7 +53,6 @@ jobs:
     - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
-        miniforge-variant: Mambaforge
         environment-file: devtools/conda-envs/test_env.yaml
         activate-environment: test_env
         channel-priority: true

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     -   id: end-of-file-fixer
         types: [python]
     -   id: trailing-whitespace
         types: [python]
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
         language_version: python3

AUTHORS

@@ -4,18 +4,18 @@ in collaboration with Daniel Zuckerman ([email protected])
 The original version of WESTPA was written by Matthew Zwier ([email protected]) 
 as part of his Ph.D. dissertation with Lillian Chong.
 
-Other contributors are the following (In alphabetical order)
+Other core contributors are the following (in alphabetical order)
 
 Joshua Adelman
-Alex DeGrave
-Page Harrison
-Joseph Kaus
-Patrick Pisciuneri
-A. J. Pratt
-Nicholas Rego
+Anthony Bogetti
+Jeremy Leung
+AJ Pratt
+John Russo
 Ali Saglam
-David Wang
+Jeff Thompson
 Kim Wong
+Darian Yang
+She Zhang
 
 The work manager interface is derived from the ``concurrent.futures`` module
 of Python 3.2 by Brian Quinlan, (C) 2011 the Python Software Foundation.

doc/doc_env.yaml

@@ -10,6 +10,8 @@ dependencies:
   - h5py
   - pyyaml
   - pyzmq
+  - pytables
+  - mdtraj
   - matplotlib-base
   - blessings
   - ipykernel

src/westpa/cli/tools/w_fluxanl.py

@@ -1,7 +1,6 @@
 import h5py
 import numpy as np
 from scipy.signal import fftconvolve
-from warnings import warn
 
 import westpa
 
@@ -370,7 +369,6 @@ def go(self):
 
 
 def entry_point():
-    warn('w_fluxanl is being deprecated.  Please use w_assign and w_direct instead.')
     WFluxanlTool().main()