Merge branch 'main' into p3

Author: sbillinge

.codecov.yml

@@ -0,0 +1,34 @@
+# codecov can find this file anywhere in the repo, so we don't need to clutter
+# the root folder.
+#comment: false
+
+codecov:
+  notify:
+    require_ci_to_pass: no
+
+coverage:
+  status:
+    patch:
+      default:
+        target: '70'
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: failure
+    project:
+      default: false
+      library:
+        target: auto
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: error
+        paths: '!*/tests/.*'
+
+      tests:
+        target: 97.9%
+        paths: '*/tests/.*'
+        if_not_found: success
+
+flags:
+  tests:
+    paths:
+      - tests/

.coveragerc

@@ -0,0 +1,13 @@
+[run]
+source =
+    diffpy.srmise
+[report]
+omit =
+    */python?.?/*
+    */site-packages/nose/*
+    # ignore _version.py and versioneer.py
+    .*version.*
+    *_version.py
+
+exclude_lines =
+    if __name__ == '__main__':

.flake8

@@ -0,0 +1,11 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    doc/source/conf.py
+max-line-length = 115
+# Ignore some style 'errors' produced while formatting by 'black'
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
+extend-ignore = E203

.github/workflows/docs.yml

@@ -0,0 +1,43 @@
+name: Build Documentation
+
+on:
+  push:
+    branches:
+      - main
+  release:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: build
+          auto-update-conda: true
+
+      - name: install requirements
+        run: >-
+          conda install -n build -c conda-forge
+          --file requirements/build.txt
+          --file requirements/run.txt
+          --file requirements/docs.txt
+          --quiet --yes
+
+      - name: install the package
+        run: python -m pip install . --no-deps
+
+      - name: build documents
+        run: make -C doc html
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc/build/html

.github/workflows/main.yml

@@ -0,0 +1,55 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - CI
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  miniconda:
+    name: Miniconda ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: ["ubuntu-latest"]
+    steps:
+      - name: check out diffpy.srmise
+        uses: actions/checkout@v3
+        with:
+          repository: diffpy/diffpy.srmise
+          path: .
+          fetch-depth: 0  # avoid shallow clone with no tags
+
+      - name: initialize miniconda
+        # this uses a marketplace action that sets up miniconda in a way that makes
+        # it easier to use.  I tried setting it up without this and it was a pain
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          # environment.yml file is needed by this action.  Because I don't want
+          # maintain this but rather maintain the requirements files it just has
+          # basic things in it like conda and pip
+          environment-file: ./environment.yml
+          python-version: 3
+          auto-activate-base: false
+
+      - name: install diffpy.srmise requirements
+        shell: bash -l {0}
+        run: |
+          conda config --set always_yes yes --set changeps1 no
+          conda config --add channels conda-forge
+          conda activate test
+          conda install --file requirements/run.txt
+          conda install --file requirements/test.txt
+          pip install .
+
+      - name: Validate diffpy.srmise
+        shell: bash -l {0}
+        run: |
+          conda activate test
+          coverage run -m pytest -vv -s
+          coverage report -m
+          codecov

.github/workflows/pre-commit.yml

@@ -0,0 +1,19 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+  workflow_dispatch:
+
+jobs:
+  pre-commit:
+    # pull requests are a duplicate of a branch push if within the same repo.
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --all-files

.isort.cfg

@@ -0,0 +1,4 @@
+[settings]
+line_length = 115
+multi_line_output = 3
+include_trailing_comma = True

.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+default_language_version:
+    python: python3
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit hooks
+    autofix_prs: true
+    autoupdate_branch: 'pre-commit-autoupdate'
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: monthly
+    skip: [no-commit-to-branch]
+    submodules: false
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: '\.(rst|txt)$'
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: no-commit-to-branch
+        name: Prevent Commit to Main Branch
+        args: ["--branch", "main"]
+        stages: [pre-commit]

MANIFEST.in

@@ -9,4 +9,3 @@ include doc/examples/README
 recursive-include doc/manual/source *.rst *.txt
 include doc/manual/source/conf.py
 include doc/manual/Makefile
-

devutils/prep.py

@@ -1,8 +1,10 @@
 #!/usr/bin/env python
 # Run examples and other scripts that should be updated before release.
 
-import io, os, sys
+import io
+import os
 import re
+import sys
 
 __basedir__ = os.getcwdu()
 
@@ -25,15 +27,15 @@ def test(self, call, *args, **kwds):
         except Exception, e:
             self.messages.append("%s: error, details below.\n%s" %(testname, e))
         finally:
-            os.chdir(__basedir__)    
-        
+            os.chdir(__basedir__)
+
     def report(self):
         print '==== Results of Tests ===='
         print '\n'.join(self.messages)
-        
+
 def scrubeol(directory, filerestr):
     """Use unix-style endlines for files in directory matched by regex string.
-    
+
     Parameters
     ----------
     directory - A directory to scrub
@@ -42,22 +44,22 @@ def scrubeol(directory, filerestr):
     os.chdir(directory)
     files = [re.match(filerestr, f) for f in os.listdir(".")]
     files = [f.group(0) for f in files if f]
-    
+
     for f in files:
         original = open(f)
         text = unicode(original.read())
         original.close()
-        
+
         updated = io.open(f, 'w', newline='\n')
         updated.write(text)
         updated.close()
-        
+
         print "Updated %s to unix-style endlines." %f
 
 
 def rm(directory, filerestr):
     """Delete files in directory matched by regex string.
-    
+
     Parameters
     ----------
     directory - A directory to scrub
@@ -66,20 +68,20 @@ def rm(directory, filerestr):
     os.chdir(directory)
     files = [re.match(filerestr, f) for f in os.listdir(".")]
     files = [f.group(0) for f in files if f]
-    
+
     for f in files:
         os.remove(f)
-        
+
         print "Deleted %s." %f
-    
+
 
 
 if __name__ == "__main__":
 
     # Temporarily add examples to path
     lib_path = os.path.abspath(os.path.join('..','doc','examples'))
     sys.path.append(lib_path)
-    
+
     # Delete existing files that don't necessarily have a fixed name.
     rm("../doc/examples/output", r"known_dG.*\.pwa")
     rm("../doc/examples/output", r"unknown_dG.*\.pwa")
@@ -88,7 +90,7 @@ def rm(directory, filerestr):
     examples = Test()
     test_names = ["extract_single_peak",
                   "parameter_summary",
-                  "fit_initial", 
+                  "fit_initial",
                   "query_results",
                   "multimodel_known_dG1",
                   "multimodel_known_dG2",
@@ -103,11 +105,11 @@ def rm(directory, filerestr):
         examples.test(test.run, plot=False)
 
     examples.report()
-    
+
     ### Convert output of example files to Unix-style endlines for sdist.
     if os.linesep != '\n':
         print "==== Scrubbing Endlines ===="
         # All *.srmise and *.pwa files in examples directory.
         scrubeol("../doc/examples/output", r".*(\.srmise|\.pwa)")
 
-        
+