Fixing some docs, removing code coverage

Author: emersodb

.github/workflows/integration_tests.yml

@@ -60,13 +60,4 @@ jobs:
 
       - name: Install dependencies and check code
         run: |
-          uv run pytest -m "integration_test" --cov src/midst_toolkit --cov-report=xml tests
-
-      # Uncomment this once this repo is configured on Codecov
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: VectorInstitute/midst-toolkit
-          fail_ci_if_error: true
-          verbose: true
+          uv run pytest -m "integration_test"

.github/workflows/unit_tests.yml

@@ -60,13 +60,4 @@ jobs:
 
       - name: Install dependencies and check code
         run: |
-          uv run pytest -m "not integration_test" --cov src/midst_toolkit --cov-report=xml tests
-
-      # Uncomment this once this repo is configured on Codecov
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          slug: VectorInstitute/midst-toolkit
-          fail_ci_if_error: true
-          verbose: true
+          uv run pytest -m "not integration_test"

.pre-commit-config.yaml

@@ -48,12 +48,6 @@ repos:
       types: [python]
       exclude: "tests"
 
-  - repo: https://github.com/crate-ci/typos
-    rev: v1  # v1.19.0
-    hooks:
-      - id: typos
-        args: []
-
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.9.1
     hooks:

CONTRIBUTING.md

@@ -84,3 +84,39 @@ Optional[Union[typing1, typing2]] -> typing1 | typing2 | None
 
 There is a custom script that enforces this style. It is not infallible. So if there is an issue with it please fix or
 report it to us.
+
+## Tests
+
+All tests for the library are housed in the tests folder. The unit and integration tests are run using `pytest`. These
+tests are automatically run through GitHub integrations on PRs to the main branch of this repository. PRs that fail
+any of the tests will not be eligible to be merged until they are fixed.
+
+To run all tests in the tests folder one only needs to run (with the venv active)
+```bash
+pytest .
+```
+To run a specific test with pytest, one runs
+```bash
+pytest tests/checkpointing/test_best_checkpointer.py
+```
+
+If you use VS Code for development, you can setup the tests with the testing integration so that you can run
+debugging and other IDE features. Setup will vary depending on your VS Code environment, but in your .vscode
+folder your `settings.json` might look something like
+
+``` JSON
+{
+    "python.testing.unittestArgs": [
+        "-v",
+        "-s",
+        ".",
+        "-p",
+        "test_*.py"
+    ],
+    "python.testing.pytestEnabled": true,
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestArgs": [
+        "."
+    ]
+}
+```

README.md

@@ -5,7 +5,6 @@
 [![code checks](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/code_checks.yml/badge.svg)](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/code_checks.yml)
 [![integration tests](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/integration_tests.yml/badge.svg)](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/integration_tests.yml)
 [![docs](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/docs.yml/badge.svg)](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/docs.yml)
-[![codecov](https://codecov.io/github/VectorInstitute/midst-toolkit/graph/badge.svg?token=83MYFZ3UPA)](https://codecov.io/github/VectorInstitute/midst-toolkit)
 ![GitHub License](https://img.shields.io/github/license/VectorInstitute/midst-toolkit)
 
 A toolkit for facilitating MIA resiliency testing on diffusion-model-based synthetic tabular data. Many of the attacks

codecov.yml

@@ -2,21 +2,21 @@
 
 ## Top Level Module
 
-::: aieng_template_uv
+::: midst_toolkit
     options:
       show_root_heading: true
       show_root_full_path: true
 
 ## Foo Module
 
-::: aieng_template_uv.foo
+::: midst_toolkit.foo
     options:
       show_root_heading: true
       show_root_full_path: true
 
 ## Bar Module
 
-::: aieng_template_uv.bar
+::: midst_toolkit.bar
     options:
       show_root_heading: true
       show_root_full_path: true

docs/api.md

@@ -1,54 +1,14 @@
-# Vector AI Engineering template (uv edition) repository
+# MIDST Toolkit Repository
 
-This template repository can be used to bootstrap AI Engineering project repositories
-on Github! The template is meant for python codebases since Python is the most commonly
-used language by our team.
+# MIDST Toolkit
 
-The template includes:
+----------------------------------------------------------------------------------------
 
-- [pyproject.toml](https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/)
-file to specify repository information and manage dependencies using
-[uv](https://docs.astral.sh/uv/).
+[![code checks](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/code_checks.yml/badge.svg)](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/code_checks.yml)
+[![integration tests](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/integration_tests.yml/badge.svg)](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/integration_tests.yml)
+[![docs](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/docs.yml/badge.svg)](https://github.com/VectorInstitute/midst-toolkit/actions/workflows/docs.yml)
+![GitHub License](https://img.shields.io/github/license/VectorInstitute/midst-toolkit)
 
-- [README.md](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-readmes) which should have basic information on why the project is
-useful, installation instructions and other information on how users can get started.
-
-- [.pre-commit-config.yaml](https://pre-commit.com/) for running pre-commit hooks that
-check for code-style, apply formatting, check for type hints and run tests.
-
-- [.github/pull_request_template.md](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/creating-a-pull-request-template-for-your-repository) for PRs.
-
-- [.github/ISSUE_TEMPLATE](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository) for bug reports and issues that can be raised on the repository.
-
-- [.github/workflows](https://docs.github.com/en/actions/using-workflows) for running CI
-workflows using Github actions. The template includes CI workflows for code checks,
-documentation building and releasing python packages to PyPI.
-
-- [LICENSE.md](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/licensing-a-repository) for adding a license to the project repository.
-By default, this is the [Apache-2.0 license](http://www.apache.org/licenses/). Please
-change according to your project!
-
-- [docs](https://squidfunk.github.io/mkdocs-material/) for adding project documentation. Typically
-projects should have API reference documentation, user guides and tutorials.
-
-- [CONTRIBUTING.md](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors) with basic guidelines on how others can
-contribute to the repository.
-
-- [CODE_OF_CONDUCT.md](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-code-of-conduct-to-your-project) with standards on how the community engages in
-a healthy and constructive manner.
-
-- [.gitignore](https://docs.github.com/en/get-started/getting-started-with-git/ignoring-files)
-with some standard file extensions to be ignored by git. Please add/modify as necessary.
-
-- [codecov.yml](https://docs.codecov.com/docs/codecov-yaml) for using codecov.io to
-generate code coverage information for your repository. You would need to add codecov.io
-app as an [integration to your repository](https://docs.codecov.com/docs/how-to-create-a-github-app-for-codecov-enterprise).
-
-
-If you are starting a new project, you can navigate to the [Use this template](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template) button
-on the top right corner of the [template repository home page](https://github.com/VectorInstitute/aieng-template)
-which will allow you to bootstrap your project repo using this template.
-
-Please check out the user guide page for more detailed information on using the
-template features. For existing projects, the [user guide](user_guide.md)
-can be followed to migrate to following the template more closely.
+A toolkit for facilitating MIA resiliency testing on diffusion-model-based synthetic tabular data. Many of the attacks
+included in this toolkit are based on the most success ones used in the
+[2025 SaTML MIDST Competition](https://vectorinstitute.github.io/MIDST/).

docs/index.md

@@ -135,12 +135,3 @@ The available workflows are:
 Publishing python package to PyPI. Create a `PYPI_API_TOKEN` and add it to the
 repository's actions [secret variables](https://docs.github.com/en/actions/security-guides/using-secrets-in-github-actions)
 in order to publish PyPI packages when new software releases are created on Github.
-
-The test workflows also compute coverage and upload code coverage metrics to
-[codecov.io](https://app.codecov.io/gh/VectorInstitute/aieng-template). Create a
-`CODECOV_TOKEN` and add it to the repository's actions [secret variables](https://docs.github.com/en/actions/security-guides/using-secrets-in-github-actions).
-
-!!! warning "codecov"
-    The [codecov](https://app.codecov.io/github/VectorInstitute) tool is subscribed under the free tier
-    which makes it usable only for public open-source repos. Hence, if you would like to develop in a
-    private repo, it is recommended to remove the codecov actions from the github workflow files.

docs/user_guide.md

@@ -5,7 +5,9 @@
 
 # List of files that we want to skip with this check. Currently empty.
 files_to_ignore: Set[str] = {"Empty"}
-file_types_to_ignore: Set[str] = {".png", ".pkl", ".pt", ".md", ".svg", ".ico"}
+file_types_to_ignore: Set[str] = {
+    ".png", ".pkl", ".pt", ".md", ".svg", ".ico", ".html", ".js", ".css", ".xml", ".xml.gz", ".inv"
+}
 # List of disallowed types to search for that should no longer be imported from the typing library. These types
 # have been migrated to either collections.abc or into core python
 disallowed_types = [