Assorted maintenance updates

.git-blame-ignore-revs

@@ -0,0 +1 @@
+# Add hashes of linting commits here

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/CI.yaml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.8, 3.11]  # Check against oldest and newest versions
+        python-version: [3.9, 3.11]  # Check against oldest and newest versions
         jax: ["", "_jax"]
         exclude:  # Skip win + jax
           - jax: "_jax"
@@ -35,7 +35,7 @@ jobs:
 
     steps:
     - name: Checkout the code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Additional info about the build
       shell: bash
@@ -45,12 +45,10 @@ jobs:
         ulimit -a
 
     - name: Setup Conda via Mamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: devtools/conda-envs/test_env${{ matrix.jax }}.yaml
-        environment-name: test
-        channels: conda-forge,defaults
-        extra-specs: |
+        create-args: >-
           python=${{ matrix.python-version }}
 
     - name: Install package
@@ -86,7 +84,7 @@ jobs:
         python umbrella-sampling-advanced-fes.py
 
     - name: CodeCov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -98,21 +96,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
     env:
       PACKAGE: "pymbar"
 
     steps:
     - name: Checkout the code
-      uses: actions/checkout@v1
+      uses: actions/checkout@v4
 
     - name: Setup Conda via Mamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: devtools/conda-envs/test_env.yaml
-        environment-name: test
-        channels: conda-forge,defaults
-        extra-specs: |
+        create-args: >-
           python=${{ matrix.python-version }}
 
     - name: Install linter and formatter

.gitignore

@@ -148,3 +148,5 @@ docs/pymbar-docs
 docs/_build
 tools/hash_dict.pickle
 docs/examples/generated/
+
+.DS_Store

devtools/travis-ci/push-docs-to-s3.py

@@ -14,35 +14,36 @@
 import thermopyl.version
 
 
-BUCKET_NAME = 'thermopyl.org'
+BUCKET_NAME = "thermopyl.org"
 if not thermopyl.version.release:
-    PREFIX = 'latest'
+    PREFIX = "latest"
 else:
     PREFIX = thermopyl.version.short_version
 
-if not any(d.project_name == 's3cmd' for d in pip.get_installed_distributions()):
-    raise ImportError('The s3cmd pacakge is required. try $ pip install s3cmd')
+if not any(d.project_name == "s3cmd" for d in pip.get_installed_distributions()):
+    raise ImportError("The s3cmd pacakge is required. try $ pip install s3cmd")
 # The secret key is available as a secure environment variable
 # on travis-ci to push the build documentation to Amazon S3.
-with tempfile.NamedTemporaryFile('w') as f:
-    f.write('''[default]
+with tempfile.NamedTemporaryFile("w") as f:
+    f.write(
+        """[default]
 access_key = {AWS_ACCESS_KEY_ID}
 secret_key = {AWS_SECRET_ACCESS_KEY}
-'''.format(**os.environ))
+""".format(
+            **os.environ
+        )
+    )
     f.flush()
 
-    template = ('s3cmd --guess-mime-type --config {config} '
-                'sync docs/_build/ s3://{bucket}/{prefix}/')
-    cmd = template.format(
-            config=f.name,
-            bucket=BUCKET_NAME,
-            prefix=PREFIX)
+    template = (
+        "s3cmd --guess-mime-type --config {config} " "sync docs/_build/ s3://{bucket}/{prefix}/"
+    )
+    cmd = template.format(config=f.name, bucket=BUCKET_NAME, prefix=PREFIX)
     return_val = subprocess.call(cmd.split())
 
     # Sync index file.
-    template = ('s3cmd --guess-mime-type --config {config} '
-                'sync devtools/ci/index.html s3://{bucket}/')
-    cmd = template.format(
-            config=f.name,
-            bucket=BUCKET_NAME)
+    template = (
+        "s3cmd --guess-mime-type --config {config} " "sync devtools/ci/index.html s3://{bucket}/"
+    )
+    cmd = template.format(config=f.name, bucket=BUCKET_NAME)
     return_val = subprocess.call(cmd.split())

docs/conf.py

@@ -103,7 +103,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -262,7 +262,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ("index", "pymbar.tex", "pymbar Documentation", pymbar.__maintainer__, "manual",),
+    (
+        "index",
+        "pymbar.tex",
+        "pymbar Documentation",
+        pymbar.__maintainer__,
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -285,13 +291,21 @@
 # If false, no module index is generated.
 # latex_domain_indices = True
 
-bibtex_bibfiles = ['references.bib']
+bibtex_bibfiles = ["references.bib"]
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("index", "pymbar", "pymbar Documentation", [pymbar.__maintainer__], 1,)]
+man_pages = [
+    (
+        "index",
+        "pymbar",
+        "pymbar Documentation",
+        [pymbar.__maintainer__],
+        1,
+    )
+]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -325,4 +339,3 @@
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 # texinfo_no_detailmenu = False
-

pymbar/_version.py

@@ -251,7 +251,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     # if there isn't one, this yields HEX[-dirty] (no NUM)
     describe_out, rc = run_command(
         GITS,
-        ["describe", "--tags", "--dirty", "--always", "--long", "--match", "%s*" % tag_prefix,],
+        [
+            "describe",
+            "--tags",
+            "--dirty",
+            "--always",
+            "--long",
+            "--match",
+            "%s*" % tag_prefix,
+        ],
         cwd=root,
     )
     # --long was added in git-1.5.5
@@ -294,7 +302,10 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (full_tag, tag_prefix,)
+            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
+                full_tag,
+                tag_prefix,
+            )
             return pieces
         pieces["closest-tag"] = full_tag[len(tag_prefix) :]
 

setup.py

@@ -24,13 +24,12 @@
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
     python_requires=">=3.6",
-    install_requires=["numpy>=1.12",
-                      "scipy",
-                      "numexpr",
-                      ],
+    install_requires=[
+        "numpy>=1.12",
+        "scipy",
+        "numexpr",
+    ],
     extras_require={
-        "jax": ["jaxlib;platform_system!='Windows'",
-                "jax;platform_system!='Windows'"
-                ],
+        "jax": ["jaxlib;platform_system!='Windows'", "jax;platform_system!='Windows'"],
     },
 )