initial commit

.gitlab-ci.yml

+default:
+  image: $CI_REGISTRY_IMAGE/ci-build-runner:$CI_COMMIT_REF_SLUG
+  before_script:
+    - python --version # For debugging
+  cache:
+    paths:
+      - .cache/pip
+      # Do not cache .tox, to recreate virtualenvs for every step
+
+stages:
+  - prepare
+  - lint
+  # check if this needs to be a separate step
+  # - build_extensions
+  - test
+  - package
+  - images
+  - integration
+  - publish # publish instead of deploy
+
+# Caching of dependencies to speed up builds
+variables:
+  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+
+include:
+  - template: Security/SAST.gitlab-ci.yml
+  - template: Security/Dependency-Scanning.gitlab-ci.yml
+  - template: Security/Secret-Detection.gitlab-ci.yml
+
+# Prepare image to run ci on
+trigger_prepare:
+  stage: prepare
+  trigger:
+    strategy: depend
+    include: .prepare.gitlab-ci.yml
+
+run_ruff:
+  stage: lint
+  script:
+    - tox -e ruff
+  allow_failure: false
+
+run_pylint:
+  stage: lint
+  script:
+    - tox -e pylint
+  allow_failure: false
+
+# build_extensions:
+#   stage: build_extensions
+#   script:
+#     - echo "build fortran/c/cpp extension source code"
+
+sast:
+  variables:
+    SAST_EXCLUDED_ANALYZERS:
+      brakeman, flawfinder, kubesec, nodejs-scan, phpcs-security-audit,
+      pmd-apex, security-code-scan, sobelow, spotbugs
+  stage: test
+
+dependency_scanning:
+  # override default before_script, job won't have Python available
+  before_script:
+    - uname
+
+secret_detection:
+  # override default before_script, job won't have Python available
+  before_script:
+    - uname
+
+# Basic setup for all Python versions for which we don't have a base image
+.run_unit_test_version_base:
+  before_script:
+    - python --version # For debugging
+    - python -m pip install --upgrade pip
+    - python -m pip install --upgrade tox twine
+
+# Run all unit tests for Python versions except the base image
+run_unit_tests:
+  extends: .run_unit_test_version_base
+  stage: test
+  image: python:3.${PY_VERSION}
+  script:
+    - tox -e py3${PY_VERSION}
+  parallel:
+    matrix: # use the matrix for testing
+      - PY_VERSION: [9, 10, 11, 12, 13]
+
+# Run code coverage on the base image thus also performing unit tests
+run_unit_tests_coverage:
+  stage: test
+  script:
+    - tox -e coverage
+  coverage: '/(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'
+  artifacts:
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+    paths:
+      - htmlcov/*
+
+package_files:
+  stage: package
+  artifacts:
+    expire_in: 1w
+    paths:
+      - dist/*
+  script:
+    - tox -e build
+
+package_docs:
+  stage: package
+  artifacts:
+    expire_in: 1w
+    paths:
+      - docs/build/*
+  script:
+    - tox -e docs
+
+docker_build:
+  stage: images
+  image: docker:latest
+  needs:
+    - package_files
+  tags:
+    - dind
+  before_script: []
+  script:
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+    - docker build -f docker/clocktec/Dockerfile . --build-arg BUILD_ENV=copy
+      --tag $CI_REGISTRY_IMAGE/clocktec:$CI_COMMIT_REF_SLUG
+    # enable this push line once you have configured docker registry cleanup policy
+    # - docker push $CI_REGISTRY_IMAGE/clocktec:$CI_COMMIT_REF_SLUG
+
+run_integration_tests:
+  stage: integration
+  allow_failure: true
+  needs:
+    - package_files
+  script:
+    - echo "make sure to move out of source dir"
+    - echo "install package from filesystem (or use the artefact)"
+    - echo "run against foreign systems (e.g. databases, cwl etc.)"
+    - exit 0
+
+publish_on_gitlab:
+  stage: publish
+  environment: gitlab
+  needs:
+    - package_files
+  when: manual
+  rules:
+    - if: $CI_COMMIT_TAG
+  script:
+    - echo "run twine for gitlab"
+    - |
+      TWINE_PASSWORD=${CI_JOB_TOKEN} \
+      TWINE_USERNAME=gitlab-ci-token \
+      python -m twine upload \
+      --repository-url ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi dist/*
+
+publish_on_test_pypi:
+  stage: publish
+  environment: pypi-test
+  needs:
+    - package_files
+  when: manual
+  rules:
+    - if: '$CI_COMMIT_TAG && $CI_COMMIT_REF_PROTECTED == "true"'
+  script:
+    - echo "run twine for test pypi"
+    # - |
+    #   TWINE_PASSWORD=${PIPY_TOKEN} \
+    #   TWINE_USERNAME=${PIPY_USERNAME} \
+    # TODO: replace URL with a pipy URL
+    #   python -m twine upload \
+    #   --repository-url ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi dist/*
+    - exit 1
+
+publish_on_pypi:
+  stage: publish
+  environment: pypi
+  needs:
+    - package_files
+  when: manual
+  rules:
+    - if: '$CI_COMMIT_TAG && $CI_COMMIT_REF_PROTECTED == "true"'
+  script:
+    - echo "run twine for pypi"
+    # - |
+    #   TWINE_PASSWORD=${PIPY_TOKEN} \
+    #   TWINE_USERNAME=${PIPY_USERNAME} \
+    # TODO: replace URL with a pipy URL
+    #   python -m twine upload \
+    #   --repository-url ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi dist/*
+    - exit 1
+
+publish_to_readthedocs:
+  stage: publish
+  allow_failure: true
+  environment: readthedocs
+  needs:
+    - package_docs
+  when: manual
+  rules:
+    - if: '$CI_COMMIT_TAG && $CI_COMMIT_REF_PROTECTED == "true"'
+  script:
+    - echo "scp docs/* ???"
+    - exit 1
+
+release_job:
+  stage: publish
+  image: registry.gitlab.com/gitlab-org/release-cli:latest
+  rules:
+    - if: '$CI_COMMIT_TAG && $CI_COMMIT_REF_PROTECTED == "true"'
+  script:
+    - echo "running release_job"
+  release:
+    tag_name: "$CI_COMMIT_TAG"
+    description: "$CI_COMMIT_TAG - $CI_COMMIT_TAG_MESSAGE"

.pre-commit-config.yaml

+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.18.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.6.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.5.2"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.10.1"
+    hooks:
+      - id: mypy
+        files: src|tests
+        args: ["--ignore-missing-imports"]
+        additional_dependencies:
+          - pytest
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.18"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.29.0"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs
+exclude: "tests/data/"

.prepare.gitlab-ci.yml

+stages:
+  - build
+
+build_ci_runner_image:
+  stage: build
+  image: docker
+  tags:
+    - dind
+  script:
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+    - |
+      if docker pull $CI_REGISTRY_IMAGE/ci-build-runner:$CI_COMMIT_REF_SLUG; then
+        docker build --cache-from $CI_REGISTRY_IMAGE/ci-build-runner:$CI_COMMIT_REF_SLUG --tag $CI_REGISTRY_IMAGE/ci-build-runner:$CI_COMMIT_REF_SLUG docker/ci-runner
+      else
+        docker pull $CI_REGISTRY_IMAGE/ci-build-runner:latest || true
+        docker build --cache-from $CI_REGISTRY_IMAGE/ci-build-runner:latest --tag $CI_REGISTRY_IMAGE/ci-build-runner:$CI_COMMIT_REF_SLUG docker/ci-runner
+      fi
+    - docker push $CI_REGISTRY_IMAGE/ci-build-runner:$CI_COMMIT_REF_SLUG # push the image
+    - |
+      if [[ "$CI_COMMIT_BRANCH" == "$CI_DEFAULT_BRANCH" ]]; then
+        docker image tag $CI_REGISTRY_IMAGE/ci-build-runner:$CI_COMMIT_REF_SLUG $CI_REGISTRY_IMAGE/ci-build-runner:latest
+        docker push $CI_REGISTRY_IMAGE/ci-build-runner:latest
+      fi

LICENSE

+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

MANIFEST.in

+include LICENSE
+include README.md
+
+recursive-include docs *
+recursive-exclude tests *

README.md

 # clocktec
 
-
-
 ## Getting started
 
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+To make it easy for you to get started with GitLab, here's a list of recommended
+next steps.
 
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+Already a pro? Just edit this README.md and make it your own. Want to make it
+easy? [Use the template at the bottom](#editing-this-readme)!
 
 ## Add your files
 
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
+- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file)
+      or
+      [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file)
+      files
+- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line)
+      or push an existing Git repository with the following command:
 
 ```
 cd existing_repo
@@ -42,52 +46,101 @@ Use the built-in continuous integration in GitLab.
 - [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
 - [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
 
-***
+---
 
 # Editing this README
 
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
+When you're ready to make this README your own, just edit this file and use the
+handy template below (or feel free to structure it however you want - this is
+just a starting point!). Thanks to
+[makeareadme.com](https://www.makeareadme.com/) for this template.
 
 ## Suggestions for a good README
 
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
+Every project is different, so consider which of these sections apply to yours.
+The sections used in the template are suggestions for most open source projects.
+Also keep in mind that while a README can be too long and detailed, too long is
+better than too short. If you think your README is too long, consider utilizing
+another form of documentation rather than cutting out information.
 
 ## Name
+
 Choose a self-explaining name for your project.
 
 ## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
+
+Let people know what your project can do specifically. Provide context and add a
+link to any reference visitors might be unfamiliar with. A list of Features or a
+Background subsection can also be added here. If there are alternatives to your
+project, this is a good place to list differentiating factors.
 
 ## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
+
+On some READMEs, you may see small images that convey metadata, such as whether
+or not all the tests are passing for the project. You can use Shields to add
+some to your README. Many services also have instructions for adding a badge.
 
 ## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
+
+Depending on what you are making, it can be a good idea to include screenshots
+or even a video (you'll frequently see GIFs rather than actual videos). Tools
+like ttygif can help, but check out Asciinema for a more sophisticated method.
 
 ## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
+
+Within a particular ecosystem, there may be a common way of installing things,
+such as using Yarn, NuGet, or Homebrew. However, consider the possibility that
+whoever is reading your README is a novice and would like more guidance. Listing
+specific steps helps remove ambiguity and gets people to using your project as
+quickly as possible. If it only runs in a specific context like a particular
+programming language version or operating system or has dependencies that have
+to be installed manually, also add a Requirements subsection.
 
 ## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
+
+Use examples liberally, and show the expected output if you can. It's helpful to
+have inline the smallest example of usage that you can demonstrate, while
+providing links to more sophisticated examples if they are too long to
+reasonably include in the README.
 
 ## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
+
+Tell people where they can go to for help. It can be any combination of an issue
+tracker, a chat room, an email address, etc.
 
 ## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
+
+If you have ideas for releases in the future, it is a good idea to list them in
+the README.
 
 ## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
 
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
+State if you are open to contributions and what your requirements are for
+accepting them.
+
+For people who want to make changes to your project, it's helpful to have some
+documentation on how to get started. Perhaps there is a script that they should
+run or some environment variables that they need to set. Make these steps
+explicit. These instructions could also be useful to your future self.
 
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
+You can also document commands to lint the code or run tests. These steps help
+to ensure high code quality and reduce the likelihood that the changes
+inadvertently break something. Having instructions for running tests is
+especially helpful if it requires external setup, such as starting a Selenium
+server for testing in a browser.
 
 ## Authors and acknowledgment
+
 Show your appreciation to those who have contributed to the project.
 
 ## License
+
 For open source projects, say how it is licensed.
 
 ## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+
+If you have run out of energy or time for your project, put a note at the top of
+the README saying that development has slowed down or stopped completely.
+Someone may choose to fork your project or volunteer to step in as a maintainer
+or owner, allowing your project to keep going. You can also make an explicit
+request for maintainers.

clocktec/_version.py

+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.1.dev1+g6000f15.d20241211'
+__version_tuple__ = version_tuple = (0, 1, 'dev1', 'g6000f15.d20241211')

clocktec/fit_clock_tec.py

+from __future__ import annotations
+
+import numpy as np
+
+
+def fit_clock_tec() -> np.ndarray:
+    # Dummy implementatio
+    return np.zeros(10)

pyproject.toml

+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+
+[project]
+name = "clocktec"
+authors = [
+    {name="Maaijke Mevius"},
+    {name="Cristina Cordun"},
+]
+description = "Correcting ionospheric Faraday rotation."
+readme = "README.md"
+license.file = "LICENSE"
+requires-python = ">=3.9"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Web Environment",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Internet :: WWW/HTTP",
+    "Topic :: Internet :: WWW/HTTP :: Dynamic Content",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Astronomy",
+    "Typing :: Typed",
+]
+dynamic = ["version"]
+dependencies = [
+    "numpy",
+    "lofarantpos",
+]
+
+[project.optional-dependencies]
+test = ["pytest >=6", "pytest-cov >=3"]
+dev = ["pytest >=6", "pytest-cov >=3", "tox-uv", "pre-commit", "ruff", "mypy"]
+docs = [
+    "sphinx!=1.6.6,!=1.6.7,>=1.6.5", # BSD
+    "sphinx-rtd-theme>=0.4.3", #MIT
+    "sphinxcontrib-apidoc>=0.3.0", #BSD
+    "myst-parser>=2.0", # MIT
+    "docutils>=0.17", # BSD
+    "sphinx-autoapi",
+    "sphinx_autodoc_typehints",
+]
+
+[project.urls]
+Homepage = "https://git.astron.nl/mevius/clocktec"
+"Bug Tracker" = "https://git.astron.nl/mevius/clocktec/-/issues"
+Changelog = "https://git.astron.nl/mevius/clocktec/-/releases"
+
+[project.scripts]
+
+
+[tool.hatch]
+version.source = "vcs"
+build.hooks.vcs.version-file = "clocktec/_version.py"
+
+[tool.hatch.envs.default]
+features = ["test"]
+scripts.test = "pytest {args}"
+
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+xfail_strict = true
+filterwarnings = ["error"]
+log_cli_level = "INFO"
+testpaths = ["tests"]
+
+
+[tool.coverage]
+run.source = ["clocktec"]
+report.exclude_also = ['\.\.\.', 'if typing.TYPE_CHECKING:']
+
+[tool.mypy]
+files = ["src", "tests"]
+python_version = "3.8"
+warn_unused_configs = true
+strict = true
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
+warn_unreachable = true
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+
+[[tool.mypy.overrides]]
+module = "clocktec.*"
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+
+[[tool.mypy.overrides]]
+module = "astropy.*"
+ignore_missing_imports = true
+
+[tool.ruff]
+src = ["clocktec", "tests"]
+
+[tool.ruff.lint]
+extend-select = [
+    "B",   # flake8-bugbear
+    "I",   # isort
+    "ARG", # flake8-unused-arguments
+    "C4",  # flake8-comprehensions
+    "EM",  # flake8-errmsg
+    "ICN", # flake8-import-conventions
+    "G",   # flake8-logging-format
+    "PGH", # pygrep-hooks
+    "PIE", # flake8-pie
+    "PL",  # pylint
+    "PT",  # flake8-pytest-style
+    "PTH", # flake8-use-pathlib
+    "RET", # flake8-return
+    "RUF", # Ruff-specific
+    "SIM", # flake8-simplify
+    "T20", # flake8-print
+    "UP",  # pyupgrade
+    "YTT", # flake8-2020
+    "EXE", # flake8-executable
+    "NPY", # NumPy specific rules
+    "PD",  # pandas-vet
+]
+ignore = [
+    "PLR09",   # Too many <...>
+    "PLR2004", # Magic value used in comparison
+    "ISC001",  # Conflicts with formatter
+]
+isort.required-imports = ["from __future__ import annotations"]
+# Uncomment if using a _compat.typing backport
+# typing-modules = ["clocktec._compat.typing"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["T20"]
+
+
+[tool.pylint]
+py-version = "3.9"
+ignore-paths = [".*/_version.py"]
+reports.output-format = "colorized"
+similarities.ignore-imports = "yes"
+messages_control.disable = [
+    "design",
+    "fixme",
+    "line-too-long",
+    "missing-module-docstring",
+    "missing-function-docstring",
+    "wrong-import-position",
+]

tests/test_fit_clock_tec.py

+from __future__ import annotations
+from clocktec.fit_clock_tec import fit_clock_tec
+import numpy as np
+
+
+def test_fit_clock_tec():
+    """test the clock tec fit"""
+    output = fit_clock_tec()
+    assert isinstance(output, np.ndarray)

tox.ini

+[tox]
+# Generative environment list to test all supported Python versions
+envlist = py3{9,10,11,12},ruff,format,pylint,coverage,docs,build
+minversion = 3.18.0
+
+[testenv]
+usedevelop = True
+package = wheel
+wheel_build_env = .pkg
+
+
+setenv =
+    LANGUAGE=en_US
+    LC_ALL=en_US.UTF-8
+    PYTHONWARNINGS=default::DeprecationWarning
+deps =
+    ./[test]
+    ./[dev]
+commands =
+    "{envpython}" --version
+    "{envpython}" -m pytest
+
+[testenv:coverage]
+commands =
+    "{envpython}" --version
+    "{envpython}" -m pytest --cov-report term --cov-report xml --cov-report html --cov=clocktec
+
+# Use generative name and command prefixes to reuse the same virtualenv
+# for all linting jobs.
+[testenv:{ruff,pylint,format}]
+usedevelop = False
+envdir = {toxworkdir}/linting
+deps =
+    ruff
+    pylint
+    pre-commit
+commands =
+    ruff: "{envpython}" -m ruff check clocktec --diff
+    ruff: "{envpython}" -m ruff check tests --diff
+    pylint: "{envpython}" -m pylint --version
+    pylint: "{envpython}" -m pylint --ignored-modules=astropy.units clocktec tests
+    format: "{envpython}" -m ruff format clocktec tests
+    pre-commit: "{envpython}" -m pre-commit run --all-files
+
+[testenv:docs]
+# Unset LC_ALL / LANGUAGE from testenv, would fail Sphinx otherwise
+setenv =
+deps =
+    ./
+    ./[docs]
+changedir = {toxinidir}
+commands =
+    sphinx-build -b html docs/source docs/build/html
+
+[testenv:build]
+usedevelop = False
+deps = build
+commands = "{envpython}" -m build