Initial commit

.dvc/.gitignore

@@ -0,0 +1,3 @@
+/config.local
+/tmp
+/cache

.dvcignore

@@ -0,0 +1,3 @@
+# Add patterns of files dvc should ignore, which could improve
+# the performance. Learn more at
+# https://dvc.org/doc/user-guide/dvcignore

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,35 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Data Resources**
+Please provide any data resources, such as model files, input data or configuration files associated with this issue. 
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Python version [e.g. 3.8]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/user-story.md

@@ -0,0 +1,25 @@
+---
+name: User Story
+about: Describe context and goals for providing value to users in this project.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+As a [user concerned]
+I want [goal]
+so that [reason]
+
+### Timebox [optional]
+What's the maximum amount of time that should be spent working on this? 
+
+### Definition of Done 
+A checklist of things that need to happen in order for this story to be successfully completed
+- [ ] Implement and check-in code changes
+- [ ] Test code changes
+- [ ] Documentation updated (if needed)
+- [ ] Code review 
+
+### Subtasks
+You can add additional sub-tasks if you'd like to break down the work further.

.github/workflows/python_package.yml

@@ -0,0 +1,36 @@
+name: Python package
+
+on:
+  pull_request:
+  push:
+    branches: [ $default-branch ]
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8
+          pip install .[test]
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest

.github/workflows/ruff.yml

@@ -0,0 +1,8 @@
+name: Ruff
+on: [push, pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1

.gitignore

@@ -0,0 +1,129 @@
+# 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/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/

CHANGELOG.md

@@ -0,0 +1,33 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+You should also add project tags for each release in Github, see [Managing releases in a repository](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository).
+
+## [2.0.0] - 2024-05-29
+### Added
+- Added example auto-built Sphinx documentation in the `docs` folder
+- Github workflow for running ruff linter
+- A note about conda dependencies to README
+- A note about using docker containers to README
+- Ruff as a linter for development
+### Changed
+- All build and packaging switched to use only pyproject.toml
+- Minimum python version changed to 3.10
+- Github workflow checks python versions 3.10, 3.11, 3.12
+- Updated DVC version to avoid `ImportError: cannot import name 'fsspec_loop'` in older versions
+### Removed
+- Removed setup.cfg
+
+## [1.0.0] - 2022-05-23
+### Added
+- README and CHANGELOG
+- cdstemplate packages for computing word count from input text
+- corpus_counter_script.py as a user-facing script with argparse examples
+- Tests of cdstemplate packages
+- A github workflow to trigger tests on pull request to the main branch
+- Sample text data from Project Gutenberg
+- Data Version Control stage for the corpus_counter_script.py
+- A sample Jupyter notebook that plots most frequent words the Gutenberg data

CONTRIBUTIONS.md

@@ -0,0 +1,38 @@
+# Contribution Guidelines
+This is a community-driven, open source project that welcomes all contributions. Whether you're a seasoned contributor or new to the project, we're grateful for all contributions. 
+
+## Community standards 
+
+We are an inclusive community that values open dialogue, mutual respect, and fair treatment. Every submission will be treated equally and we encourage those with diverse backgrounds and perspectives to contribute. 
+
+We are part of the University of Massachusetts Amherst, so we adhere to the [UMass Code of Student Conduct](https://www.umass.edu/dean_students/codeofconduct).
+
+## Getting started 
+Before contributing to the project, take a look at the README file, which contains information about system requirements, environment setup steps, and a project summary. 
+
+Further documentation for this project is found in the docs folder. 
+
+## Selecting an issue
+Issues that are open for contribution are given the following labels:
+- good-first-issue
+  - Issues with this tag are suited for those that do not have previous experience with the project.
+- help-wanted
+  - Issues with this tag are open for contribution and are suited for those with experience in contribution. 
+
+## Submitting contributions
+
+To contribute to the project, do the following:
+- [Fork and clone](https://docs.github.com/en/get-started/quickstart/fork-a-repo) the repository
+- Create a [branch](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-and-deleting-branches-within-your-repository) for your issue 
+- Make a [pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request) to the main branch of the upstream repository
+  - Title your pull request with the issue you fixed
+    - For example, "Fixed upload error to resolve Issue #987"
+  - Include a short description of the changes you made
+
+## Issue reporting and help
+Report bugs, issues, or suggested features to * insert email.*
+
+Direct all questions to *insert email *, but keep in mind that we are a small team and may take awhile to respond. 
+
+
+

LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 University of Massachusetts Amherst, Center for Data Science
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.