Merge pull request #6 from ResearchObject/upload-zip

Initial setup: pull metadata from crate to populate Zenodo submission

.github/workflows/lint.yml

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+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Lint with black and flake8
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
+    - 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: Lint with black
+      run: |
+        black --check --diff .

.github/workflows/test.yml

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+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Test with mypy and pytest
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: [ubuntu-latest]
+            python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
+    - name: Lint with mypy
+      run: |
+        mypy .
+    - name: Test with pytest
+      run: |
+        pytest

.gitignore

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+# 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/

docs/developer_guide.md

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+# Developer Guide - Under Construction
+
+## Environment
+
+Install dependencies:
+
+```bash
+# general dependencies
+pip install -r requirements.txt
+# dev dependencies
+pip install -r requirements-dev.txt
+```
+
+Configure Zenodo access token(s) as in [user guide - Set up a Zenodo personal access token](user_guide.md#set-up-a-zenodo-personal-access-token).
+
+## Run tests
+
+Beware that tests may make Zenodo uploads using your access token.
+
+```bash
+cd ro_crate_uploader
+pytest
+```

docs/user_guide.md

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+# User Guide - Under Construction
+
+## Install requirements
+
+```
+pip install -r requirements.txt
+```
+
+## Set up a Zenodo personal access token
+
+Create a file called `~/.config/zenodo.ini` on your computer with the following contents:
+
+```ini
+# if using the Zenodo sandbox
+[zenodo:sandbox]
+sandbox_api_token = 
+
+# if using the real Zenodo
+[zenodo]
+api_token = 
+```
+
+Now create a Zenodo access token:
+
+1. Register for a Zenodo account if you don’t already have one.
+1. Go to your profile and select Applications.
+1. You should see a section called "Personal access tokens." Click the "New token" button.
+1. Give the token a name that reminds you of what you're using it for (e.g. _RO-Crate uploader token_)
+1. Select the scopes `deposit:write` and `deposit:actions` [confirm later].
+1. Click "Create."
+1. Copy the access token into your `~/.config/zenodo.ini` file.
+
+The resulting file should look like this:
+
+```ini
+# if using the Zenodo sandbox
+[zenodo:sandbox]
+sandbox_api_token = your-sandbox-token-here
+
+# if using the real Zenodo
+[zenodo]
+api_token = your-token-here
+```
+
+`ro-crate-uploader` will read this token whenever it connects to Zenodo in order to perform actions under your account. It's recommended to use the Zenodo sandbox until you're confident using `ro-crate-uploader`.

pyproject.toml

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+[tool.mypy]
+[[tool.mypy.overrides]]
+module = "rocrate.*"
+ignore_missing_imports = true

requirements-dev.txt

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+flake8
+black
+pytest
+mypy

requirements.txt

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+zenodo-client>=0.3.3
+rocrate