fix p3

.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/action@v3.0.0
+        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
-

README.rst

@@ -5,38 +5,38 @@ SrMise
 `DiffPy project <http://www.diffpy.org>`_ tool for unbiased peak extraction from
 atomic pair distribution functions.
 
-SrMise is an implementation of the `ParSCAPE algorithm  
-<https://dx.doi.org/10.1107/S2053273315005276>`_ for peak extraction from 
-atomic pair distribution functions (PDFs).  It is designed to function even 
-when *a priori* knowledge of the physical sample is limited, utilizing the 
-Akaike Information Criterion (AIC) to estimate whether peaks are 
-statistically justified relative to alternate models.  Three basic use cases 
-are anticipated for SrMise.  The first is peak fitting a user-supplied 
-collections of peaks.  The second is peak extraction from a PDF with no (or 
-only partial) user-supplied peaks.  The third is an AIC-driven multimodeling 
-analysis where the output of multiple SrMise trials are ranked. 
-
-The framework for peak extraction defines peak-like clusters within the data, 
-extracts a single peak within each cluster, and iteratively combines nearby 
-clusters while performing a recursive search on the residual to identify 
-occluded peaks.  Eventually this results in a single global cluster 
-containing many peaks fit over all the data.  Over- and underfitting are 
+SrMise is an implementation of the `ParSCAPE algorithm
+<https://dx.doi.org/10.1107/S2053273315005276>`_ for peak extraction from
+atomic pair distribution functions (PDFs).  It is designed to function even
+when *a priori* knowledge of the physical sample is limited, utilizing the
+Akaike Information Criterion (AIC) to estimate whether peaks are
+statistically justified relative to alternate models.  Three basic use cases
+are anticipated for SrMise.  The first is peak fitting a user-supplied
+collections of peaks.  The second is peak extraction from a PDF with no (or
+only partial) user-supplied peaks.  The third is an AIC-driven multimodeling
+analysis where the output of multiple SrMise trials are ranked.
+
+The framework for peak extraction defines peak-like clusters within the data,
+extracts a single peak within each cluster, and iteratively combines nearby
+clusters while performing a recursive search on the residual to identify
+occluded peaks.  Eventually this results in a single global cluster
+containing many peaks fit over all the data.  Over- and underfitting are
 discouraged by use of the AIC when adding or, during a pruning step, removing
-peaks.  Termination effects, which can lead to physically spurious peaks in 
-the PDF, are incorporated in the mathematical peak model and the pruning step 
-attempts to remove peaks which are fit better as termination ripples due to 
-another peak. 
-
-Where possible, SrMise provides physically reasonable default values 
-for extraction parameters.  However, the PDF baseline should be estimated by 
-the user before extraction, or by performing provisional peak extraction with 
-varying baseline parameters.  The package defines a linear (crystalline) 
-baseline, arbitrary polynomial baseline, a spherical nanoparticle baseline, 
-and an arbitrary baseline interpolated from a list of user-supplied values.  
-In addition, PDFs with accurate experimentally-determined uncertainties are 
-necessary to provide the most reliable results, but historically such PDFs 
-are rare.  In the absence of accurate uncertainties an *ad hoc* uncertainty 
-must be specified. 
+peaks.  Termination effects, which can lead to physically spurious peaks in
+the PDF, are incorporated in the mathematical peak model and the pruning step
+attempts to remove peaks which are fit better as termination ripples due to
+another peak.
+
+Where possible, SrMise provides physically reasonable default values
+for extraction parameters.  However, the PDF baseline should be estimated by
+the user before extraction, or by performing provisional peak extraction with
+varying baseline parameters.  The package defines a linear (crystalline)
+baseline, arbitrary polynomial baseline, a spherical nanoparticle baseline,
+and an arbitrary baseline interpolated from a list of user-supplied values.
+In addition, PDFs with accurate experimentally-determined uncertainties are
+necessary to provide the most reliable results, but historically such PDFs
+are rare.  In the absence of accurate uncertainties an *ad hoc* uncertainty
+must be specified.
 
 For more information about SrMise, see the users manual at
 http://diffpy.github.io/diffpy.srmise.
@@ -65,7 +65,7 @@ individual and/or academic use, but some also have commercial version.  Links to
 executables, installation instructions, and licensing information
 for some popular options are listed below.
 
-* `Anaconda <http://www.continuum.io/downloads>`_
+* `Anaconda <https://www.anaconda.com/download>`_
 * `Enthought Canopy <https://www.enthought.com/products/canopy/>`_
 * `Python(x,y) <https://code.google.com/p/pythonxy/>`_
 * `WinPython <http://winpython.github.io>`_
@@ -120,7 +120,7 @@ in MacPorts::
 
 The simplest way to obtain diffpy.srmise on Mac OS X systems
 is using ``pip`` to download and install the latest release from
-`PyPI <https://pypi.python.org>`_. :: 
+`PyPI <https://pypi.python.org>`_. ::
 
    sudo pip install diffpy.srmise
 
@@ -131,9 +131,9 @@ Uncompress them to a directory, and from that directory run ::
 
    sudo python setup.py install
 
-This installs diffpy.srmise for all users in the default system location. If 
-administrator (root) access is not available, see the usage info from 
-``python setup.py install --help`` for options to install to user-writable 
+This installs diffpy.srmise for all users in the default system location. If
+administrator (root) access is not available, see the usage info from
+``python setup.py install --help`` for options to install to user-writable
 directories.
 
 
@@ -154,7 +154,7 @@ For other Linux distributions consult the appropriate package manager.
 
 The simplest way to obtain diffpy.srmise on Linux systems
 is using ``pip`` to download and install the latest release from the
-`PyPI <https://pypi.python.org>`_. :: 
+`PyPI <https://pypi.python.org>`_. ::
 
    sudo pip install diffpy.srmise
 
@@ -165,24 +165,24 @@ Uncompress them to a directory, and from that directory run ::
 
    sudo python setup.py install
 
-This installs diffpy.srmise for all users in the default system location. If 
-administrator (root) access is not available, see the usage info from 
-``python setup.py install --help`` for options to install to user-writable 
-directories. 
+This installs diffpy.srmise for all users in the default system location. If
+administrator (root) access is not available, see the usage info from
+``python setup.py install --help`` for options to install to user-writable
+directories.
 
 
 DEVELOPMENT
 ===========
 
-diffpy.srmise is open-source software developed with support of the Center of 
-Research Excellence in Complex Materials at Michigan State University, in 
-cooperation with the DiffPy-CMI complex modeling initiative at the Brookhaven 
-National Laboratory.  The diffpy.srmise sources are hosted at 
-https://github.com/diffpy/diffpy.srmise. 
+diffpy.srmise is open-source software developed with support of the Center of
+Research Excellence in Complex Materials at Michigan State University, in
+cooperation with the DiffPy-CMI complex modeling initiative at the Brookhaven
+National Laboratory.  The diffpy.srmise sources are hosted at
+https://github.com/diffpy/diffpy.srmise.
 
-Feel free to fork the project and contribute.  To install diffpy.srmise in a 
-development mode, with its sources being directly used by Python rather than 
-copied to a package directory, use :: 
+Feel free to fork the project and contribute.  To install diffpy.srmise in a
+development mode, with its sources being directly used by Python rather than
+copied to a package directory, use ::
 
    python setup.py develop --user