miniff issueshttps://gitlab.kwant-project.org/qt/miniff/-/issues2021-06-25T16:52:59Zhttps://gitlab.kwant-project.org/qt/miniff/-/issues/5Refine installation instructions2021-06-25T16:52:59ZArtem PulkinRefine installation instructions- Add Windows-specific instructions
- Work around possible names for `openmp` library during `Cython` code linking- Add Windows-specific instructions
- Work around possible names for `openmp` library during `Cython` code linkinghttps://gitlab.kwant-project.org/qt/miniff/-/issues/2Suggestion: switch to pytest2021-04-28T16:16:25ZAnton AkhmerovSuggestion: switch to pytestnose is unmaintained and recommends to use pytest insteadnose is unmaintained and recommends to use pytest insteadhttps://gitlab.kwant-project.org/qt/miniff/-/issues/19Implementing typical workflows2021-04-23T10:17:11ZArtem PulkinImplementing typical workflowsThe package requires putting things together into workflows which can be executed in CLI. Initial workflow implementation has been done with a1a42f8df7cbdaec6a59550b315985d07330c733. This issue is here to track additional features to be ...The package requires putting things together into workflows which can be executed in CLI. Initial workflow implementation has been done with a1a42f8df7cbdaec6a59550b315985d07330c733. This issue is here to track additional features to be implemented.
TODO:
- CLI
- workflow serializationhttps://gitlab.kwant-project.org/qt/miniff/-/issues/36Add a landing page2021-04-21T15:23:52ZArtem PulkinAdd a landing pagehttps://gitlab.kwant-project.org/qt/miniff/-/issues/11Enable software citation2021-04-13T06:31:36ZNiket AgrawalEnable software citationGenerate a Digital object Identifier (DOI) for the software, thus enabling its proper citation in research papers or other scientific works that may use it in future. Discuss and choose a solution, for example, Zenodo.Generate a Digital object Identifier (DOI) for the software, thus enabling its proper citation in research papers or other scientific works that may use it in future. Discuss and choose a solution, for example, Zenodo.https://gitlab.kwant-project.org/qt/miniff/-/issues/32Synchronize minimal package versions across different places2021-03-31T13:04:12ZArtem PulkinSynchronize minimal package versions across different placesThere are several places where package versions were specified:
1. ``environment.yml``
2. ``pyproject.toml``
3. ``.gitlab.ci``
4. ``requirements.txt``
5. condaThere are several places where package versions were specified:
1. ``environment.yml``
2. ``pyproject.toml``
3. ``.gitlab.ci``
4. ``requirements.txt``
5. condaNiket AgrawalNiket Agrawalhttps://gitlab.kwant-project.org/qt/miniff/-/issues/31Create a project handover documentation2021-03-30T09:16:38ZNiket AgrawalCreate a project handover documentationCreate a documentation for project handover purposes. This document will serve the purpose of a reference manual to the maintainer(s) of miniff. It shall provides the following information.
- Implementation and configuration details of ...Create a documentation for project handover purposes. This document will serve the purpose of a reference manual to the maintainer(s) of miniff. It shall provides the following information.
- Implementation and configuration details of certain aspects of the repository such as the documentation setup, versioning, packaging, CI and dependency management.
- Software development and maintenance workflow for miniff.
The aforementioned details will be captured in the Wiki of the miniff GitLab repositoryNiket AgrawalNiket Agrawalhttps://gitlab.kwant-project.org/qt/miniff/-/issues/30Remove patch version number pinning to facilitate receiving bug fixes for the...2021-03-09T09:37:17ZNiket AgrawalRemove patch version number pinning to facilitate receiving bug fixes for the packagesNot fixing the patch version number facilitates receiving bug fixes for individual packages by requirements.txt/env.yml and update the environment. The overall consistency is still maintained as the major and minor version numbers remain...Not fixing the patch version number facilitates receiving bug fixes for individual packages by requirements.txt/env.yml and update the environment. The overall consistency is still maintained as the major and minor version numbers remain fixed.Niket AgrawalNiket Agrawalhttps://gitlab.kwant-project.org/qt/miniff/-/issues/14Upload miniff on PyPI2021-03-04T10:12:42ZNiket AgrawalUpload miniff on PyPIUploading and making the miniff software package available on PyPI will provide one step installation for users.Uploading and making the miniff software package available on PyPI will provide one step installation for users.Niket AgrawalNiket Agrawalhttps://gitlab.kwant-project.org/qt/miniff/-/issues/28Update installation instructions in README to include pip install miniff2021-02-23T09:53:42ZNiket AgrawalUpdate installation instructions in README to include pip install miniffNow that miniff is uploaded to PyPI, single command installation via pip, i.e., `pip install miniff` suffices for the end users who wish to install and use miniff, they need not set up a development environment explicitly which the curre...Now that miniff is uploaded to PyPI, single command installation via pip, i.e., `pip install miniff` suffices for the end users who wish to install and use miniff, they need not set up a development environment explicitly which the current README instructs to do. That is meant for developers who wish to contribute to miniff and is already covered in CONTRIBUTING.md.Niket AgrawalNiket Agrawalhttps://gitlab.kwant-project.org/qt/miniff/-/issues/13Add CONTRIBUTING.md containing instructions for contributing to the code and ...2021-02-15T13:29:51ZNiket AgrawalAdd CONTRIBUTING.md containing instructions for contributing to the code and also the documentationAdd CONTRIBUTING.md containing instructions for contributing to the code and also the documentation. These instructions should be separated from the README.md and put explicitly in this file.Add CONTRIBUTING.md containing instructions for contributing to the code and also the documentation. These instructions should be separated from the README.md and put explicitly in this file.Niket AgrawalNiket Agrawalhttps://gitlab.kwant-project.org/qt/miniff/-/issues/27Add a changelog2021-02-15T13:25:27ZNiket AgrawalAdd a changelogAdd a changelog to keep an ordered history of changes in each version of miniffAdd a changelog to keep an ordered history of changes in each version of miniffNiket AgrawalNiket Agrawalhttps://gitlab.kwant-project.org/qt/miniff/-/issues/25Build docs in CI2021-01-25T16:17:36ZArtem PulkinBuild docs in CIArtem PulkinArtem Pulkinhttps://gitlab.kwant-project.org/qt/miniff/-/issues/3Remove `dfttools` dependency2021-01-25T11:30:27ZArtem PulkinRemove `dfttools` dependency`dfttools` is not in package indexes and only a small part of it (`UnitCell`) is used.
- Include a minimal prototype of `UnitCell` into the package;
- Remove the dependency.`dfttools` is not in package indexes and only a small part of it (`UnitCell`) is used.
- Include a minimal prototype of `UnitCell` into the package;
- Remove the dependency.https://gitlab.kwant-project.org/qt/miniff/-/issues/24Migrate the read the docs webhook for documentation hosting to one of the gro...2021-01-25T11:26:42ZNiket AgrawalMigrate the read the docs webhook for documentation hosting to one of the group member's read the docs accountAt present, the webhook for continuous documentation build and hosting on read the docs (rtd) is temporarily configured under the rtd account of the DCC staff member. This needs to be migrated to the rtd account of one of the group membe...At present, the webhook for continuous documentation build and hosting on read the docs (rtd) is temporarily configured under the rtd account of the DCC staff member. This needs to be migrated to the rtd account of one of the group members.
Steps to perform the migration:
- Delete the existing rtd webhook in gitlab. To do this, go to Miniff Gitlab repository > Settings > Webhooks. At the bottom of the page you will see two project hooks, the first one is for the rtd documentation and needs to be removed by clicking on delete.
- Then, the miniff repository needs to be imported in your read the docs account. See instructions [here](https://docs.readthedocs.io/en/stable/intro/import-guide.html)
- A webhook needs to be created on the miniff gitlab repository for enabling automated build and update of documentation by rtd. See instructions [here](https://docs.readthedocs.io/en/stable/webhooks.html)
- By default, rtd tracks changes and builds the documentation on the master branch. You can test the webhook by triggering a build from the rtd web dashboard.Artem PulkinArtem Pulkinhttps://gitlab.kwant-project.org/qt/miniff/-/issues/22Docs failing to build in master2021-01-25T11:25:50ZNiket AgrawalDocs failing to build in masterThe docs fail to build because the computing descriptor tutorial is no longer able to import UnitCell.
Steps to reproduce:
1. Clone miniff repostory, checkout master, step into the `docs/` directory and build the docs by executing `make...The docs fail to build because the computing descriptor tutorial is no longer able to import UnitCell.
Steps to reproduce:
1. Clone miniff repostory, checkout master, step into the `docs/` directory and build the docs by executing `make html`
```
cd miniff/docs/
make html
```
Below error is seen at the output.
```
~/dressing-up-ML-code/miniff/docs/design.rst:2: WARNING: Title underline too short.
Miniff Design Documentation
====================
~/dressing-up-ML-code/miniff/docs/design.rst:27: WARNING: Unexpected indentation.
~/dressing-up-ML-code/miniff/docs/design.rst:27: WARNING: Inline interpreted text or phrase reference start-string without end-string.
~/dressing-up-ML-code/miniff/docs/design.rst:30: WARNING: Block quote ends without a blank line; unexpected unindent.
Extension error:
Cell raised uncaught exception:
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-6-4d95605925b0> in <module>
----> 1 from miniff.kernel import UnitCell, NeighborWrapper
2
3 cell = UnitCell(np.eye(3), r, 'a')
ImportError: cannot import name 'UnitCell' from 'miniff.kernel' (~/miniconda3/envs/dressingupmlcode/lib/python3.8/site-packages/miniff-0.1.0-py3.8-linux-x86_64.egg/miniff/kernel.py)
make: *** [Makefile:20: html] Error 2
```https://gitlab.kwant-project.org/qt/miniff/-/issues/20Testing with different package versions2021-01-22T18:23:54ZArtem PulkinTesting with different package versionsIt is better to support a range of dependency versions and to test several version configurations in CI.It is better to support a range of dependency versions and to test several version configurations in CI.https://gitlab.kwant-project.org/qt/miniff/-/issues/23CI failing on master due to missing imports in test_optimization.py2021-01-22T14:04:16ZNiket AgrawalCI failing on master due to missing imports in test_optimization.pyCI is failing on latest master due to missing import statements in the file test_optimization.py.CI is failing on latest master due to missing import statements in the file test_optimization.py.https://gitlab.kwant-project.org/qt/miniff/-/issues/10Add license2021-01-22T14:03:36ZNiket AgrawalAdd licenseAdd a license to facilitate software distribution, allow others to utilize this code, build on top of this code, etc.Add a license to facilitate software distribution, allow others to utilize this code, build on top of this code, etc.Anton AkhmerovAnton Akhmerovhttps://gitlab.kwant-project.org/qt/miniff/-/issues/9Dependency management for easy reproducibility2021-01-21T17:35:56ZNiket AgrawalDependency management for easy reproducibilityCurrently, the dependencies needs to be installed one by one and the steps are specific to pip users.
To Do:
1. Implement an approach for managing dependencies that make miniff environment reproducibility and installation convenient a...Currently, the dependencies needs to be installed one by one and the steps are specific to pip users.
To Do:
1. Implement an approach for managing dependencies that make miniff environment reproducibility and installation convenient and straightforward.
2. Update the Readme with the usage and installation instructions accordingly.Niket AgrawalNiket Agrawal