dso-core 0.8.2.post2__tar.gz

dso_core-0.8.2.post2/.cruft.json

@@ -0,0 +1,30 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "4c8f4683073074b201a45b173d91b2a352d4a194",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "dso-core",
+      "package_name": "dso",
+      "project_description": "data science operations",
+      "author_full_name": "Gregor Sturm",
+      "author_email": "gregor.sturm@boehringer-ingelheim.com",
+      "github_user": "sturmgre",
+      "github_repo": "dso",
+      "license": "MIT License",
+      "ide_integration": true,
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null
+}

dso_core-0.8.2.post2/.editorconfig

@@ -0,0 +1,15 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab

dso_core-0.8.2.post2/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,35 @@
+name: Bug report
+description: File a bug report if DSO is breaking / not behaving in the way you expect
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of bug
+      description: |
+        A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: log
+    attributes:
+      label: DSO Error log
+      description: |
+        Please paste your **full command** and DSO log.
+      render: console
+      placeholder: |
+        $ dso
+
+  - type: checkboxes
+    id: checklist
+    attributes:
+      label: Before submitting
+      description: >-
+        Please ensure your bug report fulfills all of the following requirements.
+      options:
+        - label: >-
+            I am using the latest release of DSO.
+          required: true
+        - label: >-
+            I have included a full DSO log, not truncated.
+          required: true

dso_core-0.8.2.post2/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,10 @@
+name: Feature request
+description: Suggest an idea for DSO
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

dso_core-0.8.2.post2/.github/workflows/pre_commit.yml

@@ -0,0 +1,26 @@
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: pre-commit
+
+jobs:
+  pre-commit:
+    permissions:
+      # Give the default GITHUB_TOKEN write permission to commit and push the
+      # added or changed files to the repository.
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+
+      - uses: pre-commit/action@v2.0.3
+
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        if: '!cancelled()'
+        with:
+          commit_message: pre-commit autofixes

dso_core-0.8.2.post2/.github/workflows/release.yml

@@ -0,0 +1,29 @@
+name: Release to PyPI
+
+on:
+  release:
+    types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/dso-core
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+          cache: "pip"
+      - run: pip install build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

dso_core-0.8.2.post2/.github/workflows/unit_tests.yml

@@ -0,0 +1,51 @@
+name: "Unit tests for DSO"
+on:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - "docs/**"
+  pull_request:
+    paths-ignore:
+      - "docs/**"
+
+jobs:
+  unit_tests_linux:
+    name: "Python ${{ matrix.python-version }}"
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    env:
+      # GitHub currently has 4 cores available for Linux runners
+      # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
+      worker_cores: 4
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: "Set up Python ${{ matrix.python-version }}"
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Install libgit2 header files for libgit2 & pandoc for testing purposes
+        run: sudo apt-get install -y libgit2-dev pandoc
+
+      - name: "Install DSO"
+        run: pip install -e '.[test]'
+
+      - name: "Run unit tests"
+        run: pytest -vv tests -n ${{ env.worker_cores }} --cov=dso --cov-report=xml
+
+      # - name: "Upload coverage to Codecov"
+      #   uses: codecov/codecov-action@v4
+      #   with:
+      #     files: ./coverage.xml
+      #   env:
+      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

dso_core-0.8.2.post2/.gitignore

@@ -0,0 +1,20 @@
+# Temp files
+.DS_Store
+*~
+buck-out/
+
+# Compiled files
+.venv/
+__pycache__/
+.*cache/
+
+# Distribution / packaging
+/dist/
+
+# Tests and coverage
+/data/
+/node_modules/
+
+# docs
+/docs/generated/
+/docs/_build/

dso_core-0.8.2.post2/.pre-commit-config.yaml

@@ -0,0 +1,47 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.16.0
+repos:
+#   - repo: https://github.com/pre-commit/mirrors-prettier
+#     rev: v4.0.0-alpha.8
+#     hooks:
+#       - id: prettier
+#         exclude: '^src/dso/templates/.*\.yaml$' # prettier messes with jinja2 templating here
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.8
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: "2.2.4"
+    hooks:
+      - id: pyproject-fmt
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

dso_core-0.8.2.post2/.prettierrc.yaml

@@ -0,0 +1,7 @@
+overrides:
+  # JSON with comments and trailing commas
+  - files: .vscode/*.json
+    options:
+      parser: json5
+      quoteProps: preserve
+      singleQuote: false

dso_core-0.8.2.post2/.vscode/extensions.json

@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "esbenp.prettier-vscode",
+    ],
+}

dso_core-0.8.2.post2/.vscode/launch.json

@@ -0,0 +1,33 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--color=yes",
+            },
+            "presentation": {
+                "hidden": true,
+            },
+        },
+    ],
+}

dso_core-0.8.2.post2/.vscode/settings.json

@@ -0,0 +1,18 @@
+{
+    "[python][jsonc][yaml]": {
+        "editor.formatOnSave": true,
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.codeActionsOnSave": {
+            "source.fixAll": "always",
+            "source.organizeImports": "always",
+        },
+    },
+    "[jsonc][yaml]": {
+        "editor.defaultFormatter": "esbenp.prettier-vscode",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}

dso_core-0.8.2.post2/CHANGELOG.md

@@ -0,0 +1,186 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog][],
+and this project adheres to [Semantic Versioning][].
+
+[keep a changelog]: https://keepachangelog.com/en/1.0.0/
+[semantic versioning]: https://semver.org/spec/v2.0.0.html
+
+
+## v0.8.2
+
+### Fixes
+
+-   Fixed params.yaml sorting issue - params.yaml order will be kept intact when using `dso get-config`
+
+## v0.8.1
+
+### Fixes
+
+-   Fixed and issue with spaces in image filenames when watermarking a quarto document
+
+## v0.8.0
+
+### New Features
+
+-   `dso init` and `dso create folder` now also work in existing directories. In such case missing files will be added
+    from the template, but existing files are never overwritten.
+-   There's now a template for a bash stage available in `dso create stage`. The stage template needs can be specified
+    via the `--template` flag, otherwise the user is prompted to choose a template.
+-   `dso` now has flags to control logging verbosity. The default log-level is `info`. `-q` will set it to `warning`,
+    `-qq` to `error` and `-v` to `debug`. The "quiet" option can also be activated by setting the environment variable
+    `DSO_QUIET=1` or `DSO_QUIET=2`.
+-   `dso exec` and `dso get-config` now have a `--skip-compile` flag to disable automatic internal calls to
+    `dso compile-config`. The flag can also be activated by setting the environment variable `DSO_SKIP_COMPILE=1`.
+
+### Fixes
+
+-   Fix that compile-config also compiles parents when in a directory without a `params.in.yaml` file.
+-   The order of dictionaries is now preserved by `dso get-config`.
+-   When running `dso init` or `dso create`, `dso compile-config` is now only executed
+    after it was clearly communicated with the user that the project/stage/folder was successfully created.
+-   Specifying a stylesheet using `css` via `dso.quarto` is now possible.
+-   Adjusted the log level of some messages to more reasonable defaults. Some messages that were previously `info`
+    messages are now `debug` messages and not shown by default.
+-   When running `dso repro`, configuration is only compiled once and not recompiled when `dso exec` or `dso get-config`
+    is called internally. This reduces runtime and redundant log messages.
+
+
+## v0.7.0
+
+-   Improved watermarking support
+
+    -   Added test cases for watermarking and the pandocfilter
+    -   Support for SVG images
+    -   There's now a `dso watermark` command line interface to watermark specified image files. In the future this
+        can be used to provide a custom plotting device in R that performs the watermarking.
+    -   Changed the watermark layout to use a tiled pattern which is less obstrusive and is guaranteed to cover the entire plot
+    -   The watermark is now fully configurable via `params.in.yaml`:
+
+        ```yaml
+        dso:
+            quarto:
+                watermark:
+                    text: WATERMARK
+                    # change the visuals - Usually fine to stick with the default, but these are the options that can be changed
+                    tile_size: [100, 100]
+                    font_size: 12
+                    font_outline: 2
+                    font_color: black
+                    font_outline_color: "#AA111160"
+        ```
+
+-   Fix issue where dso was stuck in an infinity loop while searching for a config file. Now it should fail
+    if it can't be found. To realize this the funcitonality for searching parent folders for a certain file
+    that was used in different places was refactored into a separate function.
+
+## v0.6.1
+
+-   Fix issue in `dso get-config` if multiple parameters have been used in a single line in `deps:`.
+
+## v0.6.0
+
+-   Add a `dso lint` command that performs consistency checks on dso projects. For now, only a single rule is
+    implemented, but it can be easily extended. The rule:
+    -   `DSO001`: In a quarto stage, ensure `dso::read_params` is called and stage name is correct.
+-   Logging information is now printed to STDERR instead of STDOUT
+-   Add `dso get-config <STAGE>` which will compile and print the configuration for a given stage to STDOUT.
+    Additionally, it filters the output to fields that are specified in `dvc.yaml` which forces the user
+    to declare all dependencies in `dvc.yaml`.
+-   Add automated watermarking of plots in quarto documents as experimental feature. For now, only png images are supported.
+    To enable, add to `params.in.yaml`:
+
+    -   `dso.quarto.watermark`: a text to be shown as watermark.
+    -   `dso.quarto.disclaimer.text`: a text to be shown as disclaimer box.
+    -   `dso.quarto.disclaimer.title`: title of the disclaimer box.
+
+    The disclaimer box is only shown if both text and title are set.
+
+### Migration advice
+
+-   Update `dso-r` to v0.3.0 to take advantage of `dso get-config`.
+
+-   Add the following rule to your `.pre-commit-config.yaml`:
+    ```yaml
+      - repo: local
+          hooks:
+          [...]
+          - id: lint
+              name: Run dso lint
+              entry: dso lint --skip-compile
+              language: system
+              stages: [commit]
+    ```
+
+## v0.5.0
+
+-   `dso.before_script` is now `dso.quarto.before_script`. This change has been made because different "exec" modules
+    will likely need different setup-scripts (i.e. environment modules). If the script shall be shared nevertheless,
+    this can be done with jinja templating.
+-   It is now possible to specify bibliography files in `params.in.config:dso.quarto.bibliography` using `!path`.
+-   Upon `dso repro`, the CLI asks once if the user wants to install the pre-commit hooks
+
+### Migration advice
+
+-   Move `dso.before_script` to `dso.quarto.before_script` in all your config files.
+-   Update all quarto stages to depend only on `params:dso.quarto` instead of `params:dso`. This will avoid
+    invalidating the cache unnecessarily.
+-   add `/.dso.json` to your .gitignore file
+
+## v0.4.4
+
+-   Remove confirmation before overwriting a newer `params.yaml` file - It turned out not to work well with
+    switching branches in git and led to way too many unnecessary questions.
+-   Do not fail when `dso.quarto` is `null` in `params.in.yaml` (not all cases were addressed in v0.4.3)
+
+## v0.4.3
+
+-   Fix confirmation to overwrite params.yaml
+-   Improve error message when `dso exec quarto` fails
+-   Make pre-commit hooks verbose
+-   Do not fail when `dso.quarto` is `null` in `params.in.yaml`
+
+## v0.4.2
+
+-   Update quarto template to include `dso` params as dependency
+-   Reduce the number of false-positives when asking for confirmation to overwrite params.yaml
+
+## v0.4.1
+
+-   Allow a tolerance of 1s when comparing timestamps of params.in.yaml and params.yaml
+
+## v0.4.0
+
+-   Ask for confirmation before overwriting a newer `params.yaml` file
+-   The log messages when compiling configuration files have improved
+-   Added `dso exec quarto`, a convenient wrapper to execute quarto stages
+    -   Quarto configuration/headers will be read from `params.yaml:qso.quarto`
+    -   A shell snippet specified in `params.yaml:dso.before_script` will be executed before rendering the report.
+        This is useful for setting up the environment, e.g. by loading modules
+
+## v0.3.1
+
+-   Update quarto template to be concordant with latest dso-r version
+
+## v0.3.0
+
+-   Updated quarto template to use dso code to load files
+-   `dso compile-config` now optionally supports specifying a list of paths
+-   Renamed `dso create project` to `dso init`
+-   Added `dso create folder` in addition to `dso create stage`.
+-   Currently only one template for `dso init`, `dso create folder` and `dso create stage` but prepared the project
+    to easily support multiple templates in the future
+-   Improved pre-commit config. Install it using `pre-commit install` in the project. It automatically performs some
+    consistency checks and dvc pull/push/checkout.
+
+## v0.2.0
+
+-   It's now possible to specify paths via the `!path` tag in params.in.yaml. These paths will be checked for existence
+    and automatically resolved such that they are always relative to the compiled params.yaml files.
+
+## v0.1.0
+
+-   initial prototype
+-   `dso create` command

dso_core-0.8.2.post2/CODE_OF_CONDUCT.md

@@ -0,0 +1,127 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the package maintainers via the communication channels listed in their GitHub profiles.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.