Merge pull request #39 from klauer/mnt_migrate

MNT/FIX: migrate to latest standards and fix documentation building

.coveragerc

@@ -3,9 +3,9 @@ source =
     jet_tracking
 [report]
 omit =
-    #tests
-    */tests/*
-    *test*
     #versioning
     .*version.*
     *_version.py
+    #tests
+    *test*
+    jet_tracking/tests/*

.flake8

@@ -0,0 +1,23 @@
+[flake8]
+exclude = .git,__pycache__,build,dist,jet_tracking/_version.py
+max-line-length = 88
+select = C,E,F,W,B,B950
+extend-ignore = E203, E501, E226, W503, W504
+
+# Explanation section:
+# B950
+#   This takes into account max-line-length but only triggers when the value
+#   has been exceeded by more than 10% (96 characters).
+# E203: Whitespace before ':'
+#   This is recommended by black in relation to slice formatting.
+# E501: Line too long (82 > 79 characters)
+#   Our line length limit is 88 (above 79 defined in E501).  Ignore it.
+# E226: Missing whitespace around arithmetic operator
+#   This is a stylistic choice which you'll find everywhere in pcdsdevices, for
+#   example.  Formulas can be easier to read when operators and operands
+#   have no whitespace between them.
+#
+# W503: Line break occurred before a binary operator
+# W504: Line break occurred after a binary operator
+#   flake8 wants us to choose one of the above two.  Our choice
+#   is to make no decision.

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -1 +1 @@
-jet_tracking/_version.py export-subst
+.git_archival.txt  export-subst

.github/workflows/standard.yml

@@ -0,0 +1,24 @@
+name: PCDS Standard Testing
+
+on:
+  push:
+  pull_request:
+  release:
+    types:
+      - published
+
+jobs:
+  standard:
+    uses: pcdshub/pcds-ci-helpers/.github/workflows/python-standard.yml@master
+    with:
+      # The workflow needs to know the package name.  This can be determined
+      # automatically if the repository name is the same as the import name.
+      package-name: "jet_tracking"
+      # Extras that will be installed for both conda/pip:
+      testing-extras: ""
+      # Extras to be installed only for conda-based testing:
+      conda-testing-extras: ""
+      # Extras to be installed only for pip-based testing:
+      pip-testing-extras: "PyQt5"
+      # Set if using setuptools-scm for the conda-build workflow
+      use-setuptools-scm: true

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "jet_tracking/pyqt-stylesheets"]
+	path = jet_tracking/pyqt_stylesheets
+	url = https://github.com/sommerc/pyqt-stylesheets/

.pre-commit-config.yaml

@@ -1,8 +1,13 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+exclude: |
+  (?x)^(
+    jet_tracking/_version.py|
+  )$
+
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.3.0
+    rev: v4.4.0
     hooks:
     -   id: no-commit-to-branch
     -   id: trailing-whitespace
@@ -18,11 +23,11 @@ repos:
     -   id: debug-statements
 
 -   repo: https://github.com/pycqa/flake8.git
-    rev: 3.8.4
+    rev: 6.0.0
     hooks:
     -   id: flake8
 
 -   repo: https://github.com/timothycrosley/isort
-    rev: 5.6.4
+    rev: 5.12.0
     hooks:
     -   id: isort

AUTHORS.rst

@@ -0,0 +1,13 @@
+=======
+Credits
+=======
+
+Maintainer
+----------
+
+* SLAC National Accelerator Laboratory <>
+
+Contributors
+------------
+
+Interested? See: `CONTRIBUTING.rst <CONTRIBUTING.rst>`_

CONTRIBUTING.rst

@@ -0,0 +1,103 @@
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/pcdshub/jet_tracking/issues.
+
+If you are reporting a bug, please include:
+
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "feature"
+is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+jet_tracking could always use more documentation, whether
+as part of the official jet_tracking docs, in docstrings,
+or even on the web in blog posts, articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/pcdshub/jet_tracking/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `jet_tracking` for local development.
+
+1. Fork the `jet_tracking` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone [email protected]:your_name_here/jet_tracking.git
+
+3. Install your local copy into a new conda environment. Assuming you have conda installed, this is how you set up your fork for local development::
+
+    $ conda create -n jet_tracking python=3.9 pip
+    $ cd jet_tracking/
+    $ pip install -e .
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. Install and enable ``pre-commit`` for this repository::
+
+    $ pip install pre-commit
+    $ pre-commit install
+
+6. Add new tests for any additional functionality or bugs you may have discovered.  And, of course, be sure that all previous tests still pass by running::
+
+    $ pytest -v
+
+7. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+8. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put your
+   new functionality into a function with a docstring, and add the feature to
+   the list in README.rst.
+3. The pull request should work for Python 3.9 and up. Check the GitHub Actions status
+   and make sure that the tests pass for all supported Python versions.

LICENSE.md

@@ -1,11 +1,39 @@
-Copyright (c) 2022, The Board of Trustees of the Leland Stanford Junior University, through SLAC National Accelerator Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+Copyright (c) 2023, The Board of Trustees of the Leland Stanford Junior
+University, through SLAC National Accelerator Laboratory (subject to receipt
+of any required approvals from the U.S. Dept. of Energy). All rights reserved.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
 
-(1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+(1) Redistributions of source code must retain the above copyright notice,
+    this list of conditions and the following disclaimer.
 
-(2) Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+(2) Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
 
-(3) Neither the name of the Leland Stanford Junior University, SLAC National Accelerator Laboratory, U.S. Dept. of Energy nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+(3) Neither the name of the Leland Stanford Junior University, SLAC National
+    Accelerator Laboratory, U.S. Dept. of Energy nor the names of its
+    contributors may be used to endorse or promote products derived from this
+    software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER, THE UNITED STATES GOVERNMENT, OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER, THE UNITED STATES GOVERNMENT,
+OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
+OF SUCH DAMAGE.
 
-You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code ("Enhancements") to anyone; however, if you choose to make your Enhancements available either publicly, or directly to SLAC National Accelerator Laboratory, without imposing a separate written license agreement for such Enhancements, then you hereby grant the following license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such Enhancements or derivative works thereof, in binary and source code form.
+You are under no obligation whatsoever to provide any bug fixes, patches, or
+upgrades to the features, functionality or performance of the source code
+("Enhancements") to anyone; however, if you choose to make your Enhancements
+available either publicly, or directly to SLAC National Accelerator Laboratory,
+without imposing a separate written license agreement for such Enhancements,
+then you hereby grant the following license: a non-exclusive, royalty-free
+perpetual license to install, use, modify, prepare derivative works, incorporate
+into other computer software, distribute, and sublicense such Enhancements or
+derivative works thereof, in binary and source code form.

conda-recipe/meta.yaml

@@ -1,35 +1,45 @@
-{% set data = load_setup_py_data() %}
+{% set package_name = "jet_tracking" %}
+{% set import_name = "jet_tracking" %}
+{% set version = load_file_regex(load_file=os.path.join(import_name, "_version.py"), regex_pattern=".*version = '(\S+)'").group(1) %}
 
 package:
-  name: jet_tracking
-  version : {{ data.get('version') }}
+  name: {{ package_name }}
+  version: {{ version }}
 
 source:
   path: ..
 
 build:
-  number: 1
+  number: 0
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv
 
 requirements:
   build:
-    - python {{PY_VER}}*,>=3.6
-    - setuptools
-
+  - python {{PY_VER}}*,>=3.9
+  - setuptools_scm
+  - pip
   run:
-    - python {{PY_VER}}*,>=3.6
-    - pcdsdevices >=2.6.0
-    - matplotlib
-    - numpy
-    - ophyd >=1.5.0
-    - bluesky >=1.6.0
-    - opencv
-    - pandas
-    - scikit-image
-    - scipy
+  - python {{PY_VER}}*,>=3.9
+  - bluesky >=1.6.0
+  - matplotlib
+  - numpy
+  - opencv
+  - ophyd >=1.5.0
+  - pandas
+  - pcdsdevices >=2.6.0
+  - qimage2ndarray
+  - scikit-image
+  - scipy
 
 test:
   imports:
-    - jet_tracking
+  - jet_tracking
+  requires:
+  - pytest
+  - pytest-cov
+  - pytest-qt
+  - pyqt
 
 about:
   home: https://github.com/pcdshub/jet_tracking

dev-requirements.txt

@@ -1,5 +1,5 @@
 # These are required for developing the package (e.g. running the tests) but
 # not necessarily required for _using_ it.
-coverage
-flake8
 pytest
+pytest-cov
+pytest-qt

docs-requirements.txt

@@ -4,6 +4,6 @@ ipython
 matplotlib
 numpydoc
 sphinx
-sphinx_rtd_theme
-doctr
-doctr-versions-menu
+sphinx_rtd_theme>=1.2.0
+docs-versions-menu
+sphinxcontrib-jquery