Merge pull request westpa#337 from westpa/develop

Update westpa2 branch with newest changes

.github/workflows/build.yaml

@@ -24,13 +24,13 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [7, 8, 9, 10, 11] # sub-versions of Python
+        python-version: [8, 9, 10, 11] # sub-versions of Python
 
     steps:
       - uses: actions/checkout@v3
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.13.1
+        uses: pypa/cibuildwheel@v2.14.1
         env:
           CIBW_SKIP: "pp* *-musllinux*"
           CIBW_BUILD: "cp3${{ matrix.python-version }}-*"
@@ -76,7 +76,7 @@ jobs:
 #       - uses: actions/checkout@v3
 # 
 #       - name: Build wheels
-#         uses: pypa/cibuildwheel@v2.13.1
+#         uses: pypa/cibuildwheel@v2.14.1
 #         env:
 #           CIBW_SKIP: "pp*"
 #           CIBW_BUILD: "cp3${{ matrix.python-version }}-*"

.github/workflows/test.yaml

@@ -30,10 +30,11 @@ jobs:
           pre-commit run --all-files
 
   test:
-    name: Test on Linux, Python ${{ matrix.python-version }}
-    runs-on: ubuntu-latest
+    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    runs-on: "${{ matrix.os }}"
     strategy:
       matrix:
+        os: ["ubuntu-latest", "macos-latest"]
         python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:

.readthedocs.yml

@@ -5,15 +5,18 @@ version: 2
 formats: all
 
 build:
-  image: latest
+  os: ubuntu-22.04
+  tools:
+    python: mambaforge-4.10
 
 sphinx:
   configuration: doc/conf.py
 
-python:
-  version: 3.7
-  install:
-    - method: pip
-      path: .
 conda:
   environment: doc/doc_env.yaml
+
+python:
+  install:
+  - path: .
+    extra_requirements:
+      - doc

devtools/conda-envs/test_env.yaml

@@ -19,5 +19,5 @@ dependencies:
   # testing
   - pytest
   - pytest-cov
-  - nose
+  - pytest-rerunfailures
   - codecov

doc/README.md

@@ -14,5 +14,5 @@ Once installed, you can use the `Makefile` in this directory to compile static H
 make html
 ```
 
-The compiled docs will be in the `_build` directory and can be viewed by opening `sphinx_index.html` (which may itself 
-be inside a directory called `html/` depending on what version of Sphinx is installed).
+The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself 
+be inside a directory called `html/` depending on what version of Sphinx is installed).

doc/conf.py

@@ -35,9 +35,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.0'
+version = '2022.05'
 # The full version, including alpha/beta/rc tags.
-release = '2.0'
+release = '2022.05'
 
 
 # -- General configuration ---------------------------------------------------
@@ -70,7 +70,7 @@
 #source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'sphinx_index'
+master_doc = 'index'
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

doc/development/api.rst

@@ -3,19 +3,19 @@ WESTPA Modules API
 
 Binning
 #######
-.. automodule:: westpa.binning.assign
+.. automodule:: westpa.core.binning.assign
 
-.. automodule:: westpa.binning.bins
+.. automodule:: westpa.core.binning.bins
 
 YAMLCFG
 ########
-.. automodule:: westpa.yamlcfg
+.. automodule:: westpa.core.yamlcfg
 
 RC
 ##
-.. autoclass:: westpa._rc.WESTRC
+.. autoclass:: westpa.core._rc.WESTRC
 
 WESTPA Tools 
 ============
 
-.. automodule:: westtools
+.. automodule:: westpa.westtools

doc/doc_env.yaml

@@ -14,3 +14,6 @@ dependencies:
   - blessings
   - ipykernel
   - mpi4py
+  - sphinx
+  - sphinx-rtd-theme
+  - pip

doc/documentation/cli/w_fork.rst

@@ -43,7 +43,7 @@ general options::
 westpa.cli.tools.w\_fork module
 -------------------------------
 
-.. automodule:: westpa.cli.tools.w_fork
+.. automodule:: westpa.cli.core.w_fork
    :members:
    :undoc-members:
    :show-inheritance: