From 856f2af5304435499c7694f6b656be25c80e8725 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Thu, 29 Feb 2024 18:10:49 +0100 Subject: [PATCH 01/10] Add issue and PR templates --- .github/ISSUE_TEMPLATE/bug_report.md | 31 +++++++++++++++++++++++ .github/ISSUE_TEMPLATE/feature_request.md | 17 +++++++++++++ .github/pull_request_template.md | 22 ++++++++++++++++ 3 files changed, 70 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/bug_report.md create mode 100644 .github/ISSUE_TEMPLATE/feature_request.md create mode 100644 .github/pull_request_template.md diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000..fcdad18 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,31 @@ +--- +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 behaviour: +1. Go to '...' +2. Click on '....' +3. Scroll down to '....' +4. See error + +**Expected behaviour** +A clear and concise description of what you expected to happen. + +**tsdf version** +The version used [e.g. 0.2.0] + +**Desktop (please complete the following information):** + - OS: [e.g. Ubuntu] + - OS version [e.g. 22.04] + +**Additional context** +Please feel free to add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000..c603b8e --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,17 @@ +--- +name: Feature request +about: Suggest an idea for this project +title: '' +labels: '' +assignees: '' + +--- + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Additional context** +Add any other context or screenshots about the feature request here. \ No newline at end of file diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 0000000..78077c3 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,22 @@ +## Pull Request + +### Description +[Provide a brief description of the changes or features implemented in this pull request.] + +### Related Issue(s) +[If applicable, mention any related issues or tasks that this pull request addresses.] + +### Checklist +Please make sure to review and check the following before submitting your pull request. Remove any items that are not applicable. + +- [ ] The code follows the style guidelines of the project. +- [ ] Unit tests have been added or updated to ensure proper functionality. +- [ ] Documentation has been updated to reflect the changes (if applicable). +- [ ] The code builds and passes all existing tests. +- [ ] All commit messages are clear and descriptive. + +### Additional Notes +[Include any additional information or notes that may be helpful for reviewers.] + +### Reviewer(s) +[Tag any specific person or team responsible for reviewing this pull request, if applicable.] \ No newline at end of file From 48d4312fb293583bbf899e359114705201cff717 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Thu, 29 Feb 2024 18:10:59 +0100 Subject: [PATCH 02/10] Improve the guidelines --- CONTRIBUTING.md | 58 ++++++++++++++++++++++++++++--------------------- README.md | 6 ++++- 2 files changed, 38 insertions(+), 26 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 9ee5328..7926eec 100755 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,7 +1,6 @@ # Contributing -Contributions are welcome, and they are greatly appreciated! Every little bit -helps, and credit will always be given. +Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given. ## Types of Contributions @@ -9,34 +8,36 @@ helps, and credit will always be given. If you are reporting a bug, please include: -* Your operating system name and version. -* Any details about your local setup that might be helpful in troubleshooting. -* Detailed steps to reproduce the bug. +- Your operating system name and version. +- Any details about your local setup that might be helpful in troubleshooting. +- Detailed steps to reproduce the bug. ### Fix Bugs -Look through the GitHub issues for bugs. Anything tagged with "bug" and "help -wanted" is open to whoever wants to implement it. +Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it. ### Implement Features -Look through the GitHub issues for features. Anything tagged with "enhancement" -and "help wanted" is open to whoever wants to implement it. +Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it. ### Write Documentation -You can never have enough documentation! Please feel free to contribute to any -part of the documentation, such as the official docs, docstrings, or even -on the web in blog posts, articles, and such. +You can never have enough documentation! Feel free to contribute to any part of the documentation, including official docs, docstrings, or web content like blog posts, articles, etc. ### Submit Feedback If you are proposing a feature: -* Explain in detail how it would work. -* Keep the scope as narrow as possible, to make it easier to implement. -* Remember that this is a volunteer-driven project, and that contributions - are welcome :) +- Explain in detail how it would work. +- Keep the scope as narrow as possible, to make it easier to implement. +- Remember that this is a volunteer-driven project, and contributions are welcome :) + +## General Python Practices + +When contributing to this project, please adhere to the following Python practices: + +- Follow [PEP 8](https://www.python.org/dev/peps/pep-0008/) for style guide recommendations. +- Ensure your code is clean, efficient, and well-documented. All methods must include documentation that follows the [Google Python Style Guide](https://google.github.io/styleguide/pyguide.html), clearly describing the method's purpose, its arguments, return values, and any exceptions raised. ## Get Started! @@ -49,25 +50,32 @@ Ready to contribute? Here's how to set up `tsdf` for local development. $ poetry install ``` -3. Use `git` (or similar) to create a branch for local development and make your changes: +3. Create a branch for local development: ```console $ git checkout -b name-of-your-bugfix-or-feature ``` -4. When you're done making changes, check that your changes conform to any code formatting requirements and pass any tests. +4. Make your changes and ensure they meet the code formatting and documentation standards. + +5. Check that your changes pass all tests. + +6. Commit your changes and push to the branch: + + ```console + $ git push origin name-of-your-bugfix-or-feature + ``` -5. Commit your changes and open a pull request. +7. Submit a pull request through GitHub. ## Pull Request Guidelines -Before you submit a pull request, check that it meets these guidelines: +Before you submit a pull request, ensure it meets these guidelines: -1. The pull request should include additional tests if appropriate. -2. If the pull request adds functionality, the docs should be updated. -3. The pull request should work for all currently supported operating systems and versions of Python. +1. The pull request should include tests that prove any new functionality works as expected. +2. If the pull request adds functionality, the documentation should be updated accordingly. +3. The pull request should work for Python's currently supported versions and major operating systems. ## Code of Conduct -Please note that the `tsdf` project is released with a -Code of Conduct. By contributing to this project you agree to abide by its terms. +Please note that the `tsdf` project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms. diff --git a/README.md b/README.md index 6c81b96..962c509 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,11 @@ mkdocs gh-deploy # deploy the documentation to GitHub pages ## Contributing -Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms. +We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md) for more details on coding standards, how to get started, and the submission process. + +## Code of Conduct + +To ensure a welcoming and respectful community, all contributors and participants are expected to adhere to our [Code of Conduct](CODE_OF_CONDUCT.md). By participating in this project, you agree to abide by its terms. ## License From 6d3b41bf4b36650b6c1421d1c158247765053adc Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Thu, 29 Feb 2024 18:43:08 +0100 Subject: [PATCH 03/10] Improve templates --- .github/ISSUE_TEMPLATE/bug_report.md | 43 +++++++++++------- .github/ISSUE_TEMPLATE/feature_request.md | 30 +++++++++---- .github/pull_request_template.md | 54 ++++++++++++++++------- 3 files changed, 88 insertions(+), 39 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index fcdad18..76b2b8f 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -1,31 +1,44 @@ --- -name: Bug report +name: Bug Report about: Create a report to help us improve -title: '' -labels: '' +title: '[BUG] ' +labels: 'bug' assignees: '' --- -**Describe the bug** +**Note:** Not all fields are obligatory, but the more details you provide, the easier it will be for us to address the issue. Feel free to omit sections that you feel are not relevant to your report. + +**Describe the Bug** A clear and concise description of what the bug is. **To Reproduce** -Steps to reproduce the behaviour: +Steps to reproduce the behavior: 1. Go to '...' -2. Click on '....' -3. Scroll down to '....' +2. Click on '...' +3. Scroll down to '...' 4. See error -**Expected behaviour** +**Expected Behavior** A clear and concise description of what you expected to happen. -**tsdf version** -The version used [e.g. 0.2.0] +**Actual Behavior** +Describe what actually happened. Include screenshots, if applicable. + +**`tsdf` Version** +- The version of `tsdf` used (e.g., 0.2.0). + +**Environment Details** +- OS: [e.g., Ubuntu] +- OS Version: [e.g., 22.04] +- Python Version: [e.g., 3.8] +- Dependencies Versions: Run `pip freeze` or provide the `poetry.lock` file if possible. + +**Error Logs and Messages** +Paste any error logs or error messages encountered here. -**Desktop (please complete the following information):** - - OS: [e.g. Ubuntu] - - OS version [e.g. 22.04] +**Attempted Solutions or Workarounds** +Describe any attempted solutions or workarounds you have tried. -**Additional context** -Please feel free to add any other context about the problem here. +**Additional Context** +Add any other context about the problem here. For example, whether the issue occurs sporadically or consistently, any patterns noticed, etc. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md index c603b8e..daea73a 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -1,17 +1,31 @@ --- -name: Feature request +name: Feature Request about: Suggest an idea for this project -title: '' -labels: '' +title: '[FEATURE] ' +labels: 'enhancement' assignees: '' --- -**Is your feature request related to a problem? Please describe.** -A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] +**Note:** Not all fields are obligatory. We appreciate any and all ideas you wish to share, so please don't hesitate to submit a request even if you can't fill out every section. The more context you provide, the better we can understand and evaluate your suggestion. + +**Feature Description** +A clear and concise description of the feature you're proposing. + +**Problem and Motivation** +Please describe the problem you are facing or the limitation with the current setup. Explain the motivation behind this feature request. For example, "I'm always frustrated when [...]." **Describe the solution you'd like** -A clear and concise description of what you want to happen. +A detailed description of the feature you would like to see implemented. Include any specific functionality and how you envision it working within the existing project. + +**Describe alternatives you've considered** +A brief description of any alternative solutions or features you've considered. Why are they less desirable than your proposed solution? + +**Potential Impacts** +Discuss any potential impacts this feature may have on the project, such as performance, size, dependencies, or compatibility. + +**Examples and Mockups** +If applicable, provide examples, mockups, or code snippets to illustrate how your feature would work. This could be as simple as a brief code example or a link to a similar feature in another project. -**Additional context** -Add any other context or screenshots about the feature request here. \ No newline at end of file +**Additional Context** +Add any other context or screenshots about the feature request here. This can include use cases, benefits to other users, or any other information that might help understand the value of the feature. diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 78077c3..7715e30 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,22 +1,44 @@ -## Pull Request +--- +name: Pull Request +about: Create a pull request to contribute to the project +title: '' +labels: '' +assignees: '' -### Description -[Provide a brief description of the changes or features implemented in this pull request.] +--- -### Related Issue(s) -[If applicable, mention any related issues or tasks that this pull request addresses.] +## Description + -### Checklist -Please make sure to review and check the following before submitting your pull request. Remove any items that are not applicable. +## Related Issue(s) + -- [ ] The code follows the style guidelines of the project. -- [ ] Unit tests have been added or updated to ensure proper functionality. -- [ ] Documentation has been updated to reflect the changes (if applicable). -- [ ] The code builds and passes all existing tests. -- [ ] All commit messages are clear and descriptive. +## Type of Change + +- [ ] Bug fix +- [ ] New feature +- [ ] Enhancement to an existing feature +- [ ] Documentation update +- [ ] Other (please specify): -### Additional Notes -[Include any additional information or notes that may be helpful for reviewers.] +## How Has This Been Tested? + + +## Checklist +- [ ] I have followed the project's style guidelines. +- [ ] My code includes relevant unit tests to cover my changes. +- [ ] I have updated the documentation to reflect my changes (if applicable). +- [ ] My changes do not introduce any new warnings or errors. +- [ ] I have performed a self-review of my own code. +- [ ] All new and existing unit tests pass successfully with my changes. +- [ ] My commit messages are clear and meaningful. + +## Additional Notes + + +## Impact + + +## Reviewer(s) + -### Reviewer(s) -[Tag any specific person or team responsible for reviewing this pull request, if applicable.] \ No newline at end of file From 07b6630d80a00c611c3b1f88101c559c6f0a392b Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Fri, 1 Mar 2024 19:20:18 +0100 Subject: [PATCH 04/10] Fix the template name --- .github/{pull_request_template.md => pull_request_template.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/{pull_request_template.md => pull_request_template.md} (100%) diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md similarity index 100% rename from .github/pull_request_template.md rename to .github/pull_request_template.md From 9465c086c56cd99b253a82efae6b5ba65b0f608a Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Thu, 7 Mar 2024 15:05:16 +0100 Subject: [PATCH 05/10] Add the pytype type checker --- poetry.lock | 2949 +++++++++++++++++++++++++----------------------- pyproject.toml | 1 + pytype.cfg | 12 + 3 files changed, 1545 insertions(+), 1417 deletions(-) create mode 100644 pytype.cfg diff --git a/poetry.lock b/poetry.lock index 442a515..5a2f5c4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,44 +1,42 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. [[package]] name = "anyio" -version = "4.0.0" +version = "4.3.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"}, - {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"}, + {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"}, + {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"}, ] [package.dependencies] exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] -trio = ["trio (>=0.22)"] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.23)"] [[package]] name = "appnope" -version = "0.1.3" +version = "0.1.4" description = "Disable App Nap on macOS >= 10.9" -category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.6" files = [ - {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"}, - {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"}, + {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"}, + {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"}, ] [[package]] name = "argon2-cffi" version = "23.1.0" description = "Argon2 for Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -59,7 +57,6 @@ typing = ["mypy"] name = "argon2-cffi-bindings" version = "21.2.0" description = "Low-level CFFI bindings for Argon2" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -95,42 +92,45 @@ tests = ["pytest"] [[package]] name = "arrow" -version = "1.2.3" +version = "1.3.0" description = "Better dates & times for Python" -category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" files = [ - {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, - {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, + {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, + {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, ] [package.dependencies] python-dateutil = ">=2.7.0" +types-python-dateutil = ">=2.8.10" + +[package.extras] +doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] +test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] [[package]] name = "asttokens" -version = "2.4.0" +version = "2.4.1" description = "Annotate AST trees with source code positions" -category = "dev" optional = false python-versions = "*" files = [ - {file = "asttokens-2.4.0-py2.py3-none-any.whl", hash = "sha256:cf8fc9e61a86461aa9fb161a14a0841a03c405fa829ac6b202670b3495d2ce69"}, - {file = "asttokens-2.4.0.tar.gz", hash = "sha256:2e0171b991b2c959acc6c49318049236844a5da1d65ba2672c4880c1c894834e"}, + {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"}, + {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"}, ] [package.dependencies] six = ">=1.12.0" [package.extras] -test = ["astroid", "pytest"] +astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"] +test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"] [[package]] name = "async-lru" version = "2.0.4" description = "Simple LRU cache for asyncio" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -143,76 +143,67 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} [[package]] name = "attrs" -version = "23.1.0" +version = "23.2.0" description = 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"sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "b2b4042b3b3466add83a727c1902ae4c27dd0f40f4a66de50abdeb6acedea7c1" +content-hash = "98cb8eb1f719ab7445c992aa2daebc4fd8d7e437e07ec28713c33148a767bba7" diff --git a/pyproject.toml b/pyproject.toml index 9fbb232..71bcd80 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,6 +30,7 @@ coverage = "^7.0.0" matplotlib = "^3.6.3" mkdocs = "^1.4.2" mkdocs-jupyter = "^0.22.0" +pytype = "^2024.2.27" [tool.poetry.scripts] validate-tsdf = "tsdf.validator:main" diff --git a/pytype.cfg b/pytype.cfg new file mode 100644 index 0000000..41538f8 --- /dev/null +++ b/pytype.cfg @@ -0,0 +1,12 @@ +[pytype] +# Path to source files +inputs = . +# Path to exclude from analysis +exclude = + **/node_modules + **/venv + **/.venv + **/build + **/dist +# Python version (matches the project's runtime environment) +python_version = 3.9 From 856d24a78d34beb9c04cc7c4fa26e7330a5cddc2 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Thu, 7 Mar 2024 15:05:33 +0100 Subject: [PATCH 06/10] Fix existing typing issues --- src/tsdf/read_tsdf.py | 3 ++- src/tsdf/write_binary.py | 6 +++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/src/tsdf/read_tsdf.py b/src/tsdf/read_tsdf.py index 04e3ac3..accbe86 100644 --- a/src/tsdf/read_tsdf.py +++ b/src/tsdf/read_tsdf.py @@ -6,6 +6,7 @@ import json import os +from pathlib import Path from typing import Dict, List from tsdf import file_utils from tsdf.constants import METADATA_NAMING_PATTERN @@ -71,7 +72,7 @@ def load_metadatas_from_dir( return metadatas -def load_metadata_from_path(path: str) -> Dict[str, TSDFMetadata]: +def load_metadata_from_path(path: Path) -> Dict[str, TSDFMetadata]: """ Loads a TSDF metadata file, returns a dictionary diff --git a/src/tsdf/write_binary.py b/src/tsdf/write_binary.py index b15f830..117f4f1 100644 --- a/src/tsdf/write_binary.py +++ b/src/tsdf/write_binary.py @@ -5,16 +5,16 @@ """ import os -from typing import Any, Dict +from typing import Any, Dict, List import numpy as np import pandas as pd -from tsdf import numpy_utils +from tsdf import numpy_utils from tsdf.tsdfmetadata import TSDFMetadata def write_dataframe_to_binaries( - file_dir: str, df: pd.DataFrame, metadatas: [TSDFMetadata] + file_dir: str, df: pd.DataFrame, metadatas: List[TSDFMetadata] ) -> None: """ Save binary file based on the provided pandas DataFrame. From 03b71b60dca2023112959ff90eb8a684caaa72c5 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Thu, 7 Mar 2024 15:06:39 +0100 Subject: [PATCH 07/10] Introduce typechecking CI/CD --- .github/workflows/pytype-checking.yml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 .github/workflows/pytype-checking.yml diff --git a/.github/workflows/pytype-checking.yml b/.github/workflows/pytype-checking.yml new file mode 100644 index 0000000..f331e15 --- /dev/null +++ b/.github/workflows/pytype-checking.yml @@ -0,0 +1,25 @@ +name: pytype Type Check + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: '3.9' + + - name: Install dependencies + run: poetry install + + - name: Run pytype + run: poetry run pytype From 9aeae87ca7f6a80f2c443c53ac0e62a7ef02988b Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Thu, 7 Mar 2024 15:12:54 +0100 Subject: [PATCH 08/10] FIx the pytype GitHub action --- .github/workflows/python-package.yml | 2 +- .github/workflows/pytype-checking.yml | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 4c35164..3232925 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -5,7 +5,7 @@ name: Python package on: push: - branches: [ main, improve-docs ] + branches: [ main ] pull_request: branches: [ main ] diff --git a/.github/workflows/pytype-checking.yml b/.github/workflows/pytype-checking.yml index f331e15..e67ec04 100644 --- a/.github/workflows/pytype-checking.yml +++ b/.github/workflows/pytype-checking.yml @@ -19,7 +19,9 @@ jobs: python-version: '3.9' - name: Install dependencies - run: poetry install + run: | + python -m pip install poetry + poetry install - name: Run pytype run: poetry run pytype From 42e66ee6101b201a7093c8512282c1b21e3b4583 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Thu, 7 Mar 2024 15:33:42 +0100 Subject: [PATCH 09/10] Set root for pytype --- .github/workflows/pytype-checking.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytype-checking.yml b/.github/workflows/pytype-checking.yml index e67ec04..c4a4e95 100644 --- a/.github/workflows/pytype-checking.yml +++ b/.github/workflows/pytype-checking.yml @@ -24,4 +24,4 @@ jobs: poetry install - name: Run pytype - run: poetry run pytype + run: poetry run pytype . From 5c78bcde25fdb1ad7388cee81f8a3e7f5d39c240 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Thu, 7 Mar 2024 15:39:01 +0100 Subject: [PATCH 10/10] Introduce the type check badge --- .github/workflows/pytype-checking.yml | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pytype-checking.yml b/.github/workflows/pytype-checking.yml index c4a4e95..9739dd8 100644 --- a/.github/workflows/pytype-checking.yml +++ b/.github/workflows/pytype-checking.yml @@ -1,4 +1,4 @@ -name: pytype Type Check +name: Pytype Type Check on: push: diff --git a/README.md b/README.md index 962c509..e342d90 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ | Badges | | |:----:|----| | **Packages and Releases** | [![Latest release](https://img.shields.io/github/release/biomarkersparkinson/tsdf.svg)](https://github.com/biomarkersparkinson/tsdf/releases/latest) [![PyPI](https://img.shields.io/pypi/v/tsdf.svg)](https://pypi.python.org/pypi/tsdf/) [![Static Badge](https://img.shields.io/badge/RSD-tsdf-lib)](https://research-software-directory.org/software/tsdf) | -| **Build Status** | [![](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/) ![Python package](https://github.com/biomarkersparkinson/tsdf/workflows/Python%20package/badge.svg) | +| **Build Status** | [![](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/) ![Python package](https://github.com/biomarkersparkinson/tsdf/workflows/Python%20package/badge.svg) [![pytype Type Check](https://github.com/biomarkersParkinson/tsdf/actions/workflows/pytype-checking.yml/badge.svg)](https://github.com/biomarkersParkinson/tsdf/actions/workflows/pytype-checking.yml) | | **DOI** | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7867899.svg)](https://doi.org/10.5281/zenodo.7867899) | | **License** | [![GitHub license](https://img.shields.io/github/license/biomarkersParkinson/tsdf)](https://github.com/biomarkersparkinson/tsdf/blob/main/LICENSE) | | **Fairness** | [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/8083/badge)](https://www.bestpractices.dev/projects/8083) |