fixing joss pub table (#84)

* Updating contributing page and adding a few lines to gitignore * Small edit * adding files to paper folder for JOSS * Adding joss workflow * Making adjustments to get joss workflow to run * Minor updates to bib formatting and spacing in paper * Attempt at fixing table newlines * Another attempt * Attempt 3 * Now we are on track * Trying html unordered lists * testing a new table format * try again * attempting a picture approach * Adding JOSS status * Updating python setup action in testing workflow * Keyword search in text from reference dictionary (#46) * init file and pull sample data * add helper functions and reference dict * clean up text, tokenize, add new labels from regex function * move example into its own file, seperate out functions to use * clean functions and make generic names * clean up example * move reference dict to example_data * remove pdb * move dict out of functions file * missed import * add metrics to measure accuracy * rename other category to unknown for fair comparison * move keyword search to preprocess step, util * move add label fucntion to classify * fix imports, add comment for viz * remove temp file * change arg to dict * add keyword util * update formating * whitespace * update args to match * remove whitespace * function rename * clean up dict * add sample data * update docstring and change col dict name * clean up and use sample data in examples * add plot function * add in visualization function for confusion matrix * add more detail to dox string * clean up function to expect predicted_col * clean up example * remove whitespace * change col name from new to predicted * clean up sample data * add notebook example * add functionality to replace text in preprocessing * add text replacement step * linter * remove example .py file in favor of jupyter notebook * remove reference dict * add new csv mapping rfiles * add csv * update jupyternotebook example * use df instead of dict * remove dict * remove unused imports and functions * update jupyter notebook and remove module * remove plot * update docstrings * linter * remove whitespace * updating testing and linting workflow * Fixing minor flake8 issues from latest flake8 version * Adding links to example code in user guides and pulling some incomplete doc pages * Adding module overview to index * updating paper to show failed formatting on table * updating the gitignore with standard python ignores (#79) * [JOSS review] Updates to the documentation (#74) * Update index.rst * Remove boilerplate info (not useful) * Update .gitignore * Add Python 3.11 to test environment (#57) * Addressing various JOSS review comments * removing unneccesary min requirements file * Updating RTD docs requirements pins and updated python version used in RTD * adding additional docs requirements to setup.py variable * adding python version in req.txt note * removing docs req txt file * adding doc pins to setup py * updaing rtd yaml to use new doc reqirements location * adding pins to req.txt * adding version, copyright, and license to __init__.py * fix citation file * add version to setup.py * remove unnecessary init file * update version to 0.2.0 * removing vestigial files * remove notice folder * troubleshooting GH tests * fixing setup.py bug * replacing package name * adding missing commas * correcting "doc" extra requirement for RTD * updating author, copyright, and version in conf.py and setup.py * pacakge->module * Renaming examples to tutorials * changing examples->tutorials * [JOSS review] Update tested versions in documentation (#58) * Update tested versions in documentation * adding 3.11 to supported versions in docs --------- Co-authored-by: Kirk Bonney <[email protected]> * Docs updates (#81) * Adding statement of need and accompanying bib items * moving statement of need to landing page * renaming documentation file examples->tutorials * updating readme to reflect examples->tutorials * fixing image embedd * remove reference to statement of need page * Adding patch notes * Update .readthedocs.yml * troubleshooting rtd * rtd * Docs updates (#82) * Adding statement of need and accompanying bib items * moving statement of need to landing page * renaming documentation file examples->tutorials * updating readme to reflect examples->tutorials * fixing image embedd * remove reference to statement of need page * Adding patch notes * removing WIP docs pages * Remvoing reference to undefined reference "reqs" * Fix image embed warnings * adding noxfile for taskrunning * Expanding temrinology page * Adding structure to user guide toctree * restructuring index * Adding gallery to tutorials page * updating doc pins * fixing linting issues with noxfile * Update builddocs.yml * attempting latex table * adding dependencies * reverting to simplified markdown style table --------- Co-authored-by: charity-kwha <[email protected]> Co-authored-by: tgunda <[email protected]> Co-authored-by: Adam R. Jensen <[email protected]>
sandialabs · Oct 24, 2023 · 1ad7d73 · 1ad7d73
1 parent e5af076
commit 1ad7d73
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Showing 112 changed files with 1,031 additions and 1,786 deletions.
diff --git a/.github/workflows/builddocs.yml b/.github/workflows/builddocs.yml
@@ -28,8 +28,8 @@ jobs:
         run: sudo apt-get update -y && sudo apt-get install -y pandoc
       - uses: actions/setup-python@v2
         with: 
-          python-version: '3.8' 
-      - name: Setup Python 3.8
+          python-version: '3.11' 
+      - name: Setup Python 3.11
         run: |
           python -m pip install --upgrade pip
           python -m pip install -r requirements.txt
@@ -42,4 +42,4 @@ jobs:
       - uses: actions/upload-artifact@v3
         with:
           name: html-docs
-          path: docs/_build/html
+          path: docs/_build/html
diff --git a/.github/workflows/lint-and-test.yml b/.github/workflows/lint-and-test.yml
@@ -4,52 +4,41 @@ on: [push, pull_request]
 
 jobs:
   test:
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8]
-        requirements: [requirements.txt]
-        include:
-          - requirements: requirements-min.txt
-            python-version: 3.7
-            os: ubuntu-latest
-
-    runs-on: ${{ matrix.os }}
-
+        python-version: ['3.8', '3.9', '3.10', '3.11']
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies in ${{ matrix.requirements }}
+    - name: Install pvops
       run: |
         python -m pip install --upgrade pip
-        pip install -r ${{ matrix.requirements }}
+        pip install .
     - name: Test with pytest
       run: |
         pip install pytest pytest-cov
         pytest --cov=pvops --cov-config=.coveragerc --cov-report term-missing pvops
 
   lint:
-
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8]
-
-    runs-on: ubuntu-latest
-
+        python-version: ['3.8', '3.9', '3.10', '3.11']
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install flake8
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        pip install flake8
     - name: Lint with flake8
       run: |
-        pip install flake8
         flake8 . --count --statistics --show-source --ignore=E402,E203,E266,E501,W503,F403,F401,E402,W291,E302,W391,W292,F405,E722,W504,E121,E125,E712
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,164 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
 __pycache__/
 pvops/text/__pycache__/
 pvops/text2time/__pycache__/
@@ -6,7 +167,7 @@ docs/_build/
 .pytest_cache/
 *.py[cod]
 examples/analysis/
-examples/.ipynb_checkpoints/
+*.ipynb_checkpoints/
 *~
 pvops/.vscode/*
 pvops/text2time/.vscode

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,13 +1,18 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 sphinx:
   configuration: docs/conf.py
 
 formats: all
 
 python:
-  version: 3.7
   install:
     - method: pip
       path: .
-    - requirements: docs/requirements.txt
+      extra_requirements:
+        - doc
diff --git a/citation.CIF → CITATION.cff b/citation.CIF → CITATION.cff
@@ -11,7 +11,7 @@ authors:
     given-names: Hector
     orcid: https://orcid.org/1234
 title: "pvOps: Improving Operational Assessments through Data Fusion"
-version: 0.1.6
+version: 0.2.0
 doi: 10.5281/zenodo.4776181
 date-released: 2021-05-26
 keywords:

diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/NOTICE/datefinder_LICENSE b/NOTICE/datefinder_LICENSE