From 126c52fb3e274112ba9df607d443e83b82ebc629 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Wed, 11 Jan 2023 18:22:59 +0000 Subject: [PATCH 01/49] WIP pyproject and poetry files --- .github/workflows/pythonpublish_sdist.yml | 11 +- darwin/version/__init__.py | 15 +- poetry.lock | 1537 +++++++++++++++++++++ pyproject.toml | 122 ++ setup.cfg | 2 - setup.py | 57 - 6 files changed, 1679 insertions(+), 65 deletions(-) create mode 100644 poetry.lock create mode 100644 pyproject.toml delete mode 100644 setup.cfg delete mode 100644 setup.py diff --git a/.github/workflows/pythonpublish_sdist.yml b/.github/workflows/pythonpublish_sdist.yml index 727804101..b7fa165fc 100644 --- a/.github/workflows/pythonpublish_sdist.yml +++ b/.github/workflows/pythonpublish_sdist.yml @@ -17,11 +17,12 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install setuptools wheel twine - python setup.py sdist + pip install poetry + poetry install + poetry build - name: Publish env: - TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} - TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} + POETRY_HTTP_BASIC_PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }} + POETRY_HTTP_BASIC_PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }} run: | - twine upload dist/* + poetry publish diff --git a/darwin/version/__init__.py b/darwin/version/__init__.py index de77196f4..9bf8efa15 100644 --- a/darwin/version/__init__.py +++ b/darwin/version/__init__.py @@ -1 +1,14 @@ -__version__ = "0.8.6" +from os.path import dirname +from pathlib import Path + +from toml import load + +version_path = Path(dirname(__file__)) / ".." / ".." / "pyproject.toml" + +pyproject = load(version_path.resolve()) +version = pyproject.get("tool", {}).get("poetry", {}).get("version") + +if version is None: + raise SystemExit("Project file doesn't contain a version") + +__version__ = version diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 000000000..2ff8bebcd --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1537 @@ +# 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from = "darwin/importer/formats" }, + { include = "darwin.exporter.formats", from = "darwin/exporter/formats" }, + { include = "darwin.version", from = "darwin/version" }, +] + +[tool.poetry.scripts] +darwin = "darwin.cli:main" + +[tool.poetry.dependencies] +python = ">=3.8.0,<3.10" +argcomplete = "^2.0.0" +humanize = "^4.4.0" +numpy = "^1.24.1" +pillow = "^9.4.0" +pyyaml = ">=5.1" +requests = "^2.28.1" +rich = "^13.0.1" +dataclasses = {markers = "python_version < \"3.7\"", version = "^0.8"} +upolygon = "0.1.8" +jsonschema = "3.2.0" +deprecation = "^2.1.0" +pydantic = "^1.10.4" +orjson = "^3.8.5" + +[tool.poetry.group] + +[tool.poetry.group.test] +optional = true + +[tool.poetry.group.ml] +optional = true + +[tool.poetry.group.medical] +optional = true + + +[tool.poetry.group.test.dependencies] +response = "^0.5.0" +pytest = "^7.2.0" +pytest-describe = "^2.0.1" +scikit-learn = "^1.2.0" + +[tool.poetry.group.ml.dependencies] +scikit-learn = "^1.2.0" +torch = "^1.13.1" +torchvision = 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hash = "sha256:b60533f3f5d530e971d6737ca6d58681ee434818fab630c83a734bb10c083ce8"}, - {file = "wheel-0.38.4.tar.gz", hash = "sha256:965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac"}, -] - -[package.extras] -test = ["pytest (>=3.0.0)"] +[extras] +dev = [] +medical = [] +ml = [] +test = [] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.10" -content-hash = "6f8d58873762e19b93028f08a08c47254063340a0023506cc222539e5fd2c20d" +content-hash = "69871e95cc8aedb9881951886d3f8619327b2eb1fa4f5c8a50c86700457a5382" diff --git a/pyproject.toml b/pyproject.toml index 8299f388f..58032f495 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] -name = "darwin-py" -version = "0.8.6" # update this when you change the version - See: https://peps.python.org/pep-0440/ +name = "darwin-py-test" +version = "0.9.3" # update this when you change the version - See: https://peps.python.org/pep-0440/ description = "Library and command line interface for darwin.v7labs.com" homepage = "https://docs.v7labs.com/reference/getting-started-2" documentation = "https://darwin-py-sdk.v7labs.com/index.html" @@ -14,20 +14,10 @@ classifiers = ["Programming Language :: Python :: 3", "License :: OSI Approved : packages = [ { include = "darwin" }, - { include = "darwin.importer", from = "darwin/importer" }, - { include = "darwin.dataset", from = "darwin/dataset" }, - { include = "darwin.torch", from = "darwin/torch" }, - { include = "darwin.exporter", from = "darwin/exporter" }, - { include = "darwin.importer.formats", from = "darwin/importer/formats" }, - { include = "darwin.exporter.formats", from = "darwin/exporter/formats" }, - { include = "darwin.version", from = "darwin/version" }, ] -[tool.poetry.scripts] -darwin = "darwin.cli:main" - [tool.poetry.dependencies] -python = ">=3.8.0,<3.10" +python = ">=3.8.0,<3.11" argcomplete = "^2.0.0" humanize = "^4.4.0" numpy = "^1.24.1" @@ -42,47 +32,28 @@ deprecation = "^2.1.0" pydantic = "^1.10.4" orjson = 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"^1.2.0" +black = {markers = "python_version > \"3.9\"", version = "^22.12.0"} +isort = {markers = "python_version > \"3.9\"", version = "^5.11.4"} +mypy = {markers = "python_version > \"3.9\"", version = "^0.991"} +response = {markers = "python_version > \"3.9\"", version = "^0.5.0"} +pytest = {markers = "python_version > \"3.9\"", version = "^7.2.0"} +pytest-describe = {markers = "python_version > \"3.9\"", version = "^2.0.1"} +scikit-learn = {markers = "python_version > \"3.9\"", version ="^1.2.0"} flake8 = {markers = "python_version > \"3.9\"", version = "^6.0.0"} +flake8-pyproject = {markers = "python_version > \"3.9\"", version = "^1.2.2"} - -[tool.poetry.plugins.console_scripts] -"darwin" = "darwin.cli:main" +[tool.poetry.scripts] +darwin = "darwin.cli:main" [build-system] requires = ["poetry-core"] @@ -94,29 +65,25 @@ build-backend = "poetry.core.masonry.api" profile = "black" [tool.mypy] -# 3rd party import ignore_missing_imports = true -# dynamic typing disallow_any_unimported = true disallow_any_expr = false disallow_any_decorated = false disallow_any_explicit = true disallow_any_generics = false disallow_subclassing_any = true -# platform python_version = "3.10" -# untyped disallow_untyped_calls = true disallow_untyped_defs = true disallow_incomplete_defs = true disallow_untyped_decorators = true -# None and Optional no_implicit_optional = true -# Warnings warn_return_any = false warn_unreachable = true -# Misc pretty = true [tool.black] -line-length = 160 \ No newline at end of file +line-length = 160 + +[tool.flake8] +max-line-length = 160 \ No newline at end of file From 90f361b2c08e9140f60865b410aeb23a94a14781 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Thu, 12 Jan 2023 12:34:35 +0000 Subject: [PATCH 03/49] Revert version to actual current --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 58032f495..c5da888d8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "darwin-py-test" -version = "0.9.3" # update this when you change the version - See: https://peps.python.org/pep-0440/ +version = "0.8.6" # update this when you change the version - See: https://peps.python.org/pep-0440/ description = "Library and command line interface for darwin.v7labs.com" homepage = "https://docs.v7labs.com/reference/getting-started-2" documentation = "https://darwin-py-sdk.v7labs.com/index.html" From 633cf6a75a7244a3afc7c8d2eefb6aaa89ac080c Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Thu, 12 Jan 2023 12:34:43 +0000 Subject: [PATCH 04/49] Revert name --- .python-version | 1 + 1 file changed, 1 insertion(+) create mode 100644 .python-version diff --git a/.python-version b/.python-version new file mode 100644 index 000000000..c8cfe3959 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.10 From ac51906e39dafda10cc0fb70a8a43823d35651b1 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Thu, 12 Jan 2023 12:35:31 +0000 Subject: [PATCH 05/49] Reupdate name --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c5da888d8..b33bd3f5c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [tool.poetry] -name = "darwin-py-test" +name = "darwin-py" version = "0.8.6" # update this when you change the version - See: https://peps.python.org/pep-0440/ description = "Library and command line interface for darwin.v7labs.com" homepage = "https://docs.v7labs.com/reference/getting-started-2" From 99206af65ba54ffbd85dd29d5dae6b9e25175a41 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Thu, 12 Jan 2023 13:55:34 +0000 Subject: [PATCH 06/49] Added debugpy to dev dependencies --- poetry.lock | 791 ++++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 1 + 2 files changed, 790 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index 290c9cb9f..412b5be68 100644 --- a/poetry.lock +++ b/poetry.lock @@ -34,6 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{markers = "python_version > \"3.9\"", version = "^1.6.5"} [tool.poetry.scripts] darwin = "darwin.cli:main" From 54aaa33818e264e6e8d3f7fa038c4cf9254dd5e6 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Thu, 12 Jan 2023 14:18:43 +0000 Subject: [PATCH 07/49] Added some docs --- docs/README.md | 73 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 docs/README.md diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 000000000..db911718c --- /dev/null +++ b/docs/README.md @@ -0,0 +1,73 @@ +# Developing for `darwin-py` + +`darwin-py` uses a `pyproject.toml` file, and manages it with `poetry` + +- [Developing for `darwin-py`](#developing-for-darwin-py) + - [Development environment](#development-environment) + - [Basic poetry commands](#basic-poetry-commands) + - [Add a package to general dependencies:](#add-a-package-to-general-dependencies) + - [Add a package to one of the extras groups](#add-a-package-to-one-of-the-extras-groups) + - [Add a package to the poetry dev dependencies](#add-a-package-to-the-poetry-dev-dependencies) + - [The `pyproject.toml` file](#the-pyprojecttoml-file) + + +## Development environment + +You can either: +* Install a `poetry` environment, and work with that, or +* Install `darwin-py` using `pip` from Pypi.org, and make your own arrangements for debugging. + +The recommended setup is to install poetry, and use this to setup a dev environment: + +```sh +$ python --version # must be 3.9 or greater for development tools +$ pip install poetry +$ poetry install --extras "test ml medical dev" -G dev +``` + +This creates a `virtualenv` for the project. If you prefer, you can use `venv` by running this command before `poetry install`: + +```sh +$ python -m venv .venv +``` + +You can give it a different name if you wish, but the name `.venv` is pre-ignored in the `.gitignore` file. + + +## Basic poetry commands + +### Add a package to general dependencies: +```sh +$ poetry add [PACKAGENAME] +``` + + +### Add a package to one of the extras groups + +(these are those that are used in `pip install darwinpy[option]` type commands - ours are `test`, `ml`, `medical`, and `dev` - `dev` is for developers who don't want to use poetry - so they can install using `pip`) + +```sh +$ poetry add [PACKAGENAME] --extras="extra group names" +``` + + +Packages added this way will be installable with `pip` once a release has been made to PyPi. + + +### Add a package to the poetry dev dependencies + +```sh +$ poetry add [PACKAGENAME] -G groupname +``` + +Currently the only group is `dev` and contains dev tools for developers using `poetry`. `poetry` groups have no effect on packaging, and things installed here will not be packaged. + +## The `pyproject.toml` file + +This was a necessary change for PEP-517, but also allows us a central place to add configuration. + +Items in the `pyproject.toml` file that are grouped as `[tool.X]` are configuration settings for specific tools on the system. + +For example, settings for `mypy` static type analyser, are in the `[tool.mypy]` group. + +A plugin is installed that allows `flake8` to take its configuration from this file, even though usually it only works with `setup.cfg` and `.flake8`. \ No newline at end of file From 137918b655fb22b8b6fc335db8c6ae3f7153a65f Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Thu, 12 Jan 2023 14:26:13 +0000 Subject: [PATCH 08/49] Added ISSUE TEMPLATE because it was a good opportunity to. --- .github/ISSUE_TEMPLATE | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE diff --git a/.github/ISSUE_TEMPLATE b/.github/ISSUE_TEMPLATE new file mode 100644 index 000000000..4928b12a5 --- /dev/null +++ b/.github/ISSUE_TEMPLATE @@ -0,0 +1,40 @@ +name: Bug Report +description: File a bug report +title: "[Bug]: " +labels: ["bug", "triage"] +body: + - type: markdown + attributes: + value: | + Thanks for taking the time to fill out this bug report! + - type: input + id: contact + attributes: + label: Contact Details + description: How can we get in touch with you if we need more info? + placeholder: ex. email@example.com + validations: + required: false + - type: textarea + id: what-happened + attributes: + label: What happened? + description: Also tell us, what did you expect to happen? + placeholder: Tell us what you see! + validations: + required: true + - type: textbox + id: version + attributes: + label: What version of darwin-py were you using? + description: Run darwin-py --version at command line and paste the output here + validations: + required: true + - type: checkboxes + id: terms + attributes: + label: Code of Conduct + description: By submitting this issue, you agree to follow our [Code of Conduct](https://example.com) + options: + - label: I agree to follow this project's Code of Conduct + required: true \ No newline at end of file From 55b1556ccb2ac9e2f12acffaeb3f44cf4bd8f751 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Thu, 12 Jan 2023 14:29:34 +0000 Subject: [PATCH 09/49] Update publish script --- .github/workflows/pythonpublish_sdist.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonpublish_sdist.yml b/.github/workflows/pythonpublish_sdist.yml index b7fa165fc..a2da422bb 100644 --- a/.github/workflows/pythonpublish_sdist.yml +++ b/.github/workflows/pythonpublish_sdist.yml @@ -18,7 +18,7 @@ jobs: run: | python -m pip install --upgrade pip pip install poetry - poetry install + poetry install --extras "test ml medical dev" -G dev poetry build - name: Publish env: From 01b6ce79c12bb4b194082f756ba8d1efb683b75b Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 14:21:49 +0000 Subject: [PATCH 10/49] Version bump --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 19082fd0a..9c7d7d84d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "darwin-py" -version = "0.8.6" # update this when you change the version - See: https://peps.python.org/pep-0440/ +version = "0.8.7" # update this when you change the version - See: https://peps.python.org/pep-0440/ description = "Library and command line interface for darwin.v7labs.com" homepage = "https://docs.v7labs.com/reference/getting-started-2" documentation = "https://darwin-py-sdk.v7labs.com/index.html" From 396ea7988d5af02b8688abc52587c7215363feb3 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 14:26:39 +0000 Subject: [PATCH 11/49] Pinning numpy at 1.23.0 --- poetry.lock | 317 +++++++++++++++++++++++++++++-------------------- pyproject.toml | 2 +- 2 files changed, 191 insertions(+), 128 deletions(-) diff --git a/poetry.lock b/poetry.lock index 412b5be68..3d5aec262 100644 --- a/poetry.lock +++ b/poetry.lock @@ -83,19 +83,102 @@ files = [ [[package]] name = "charset-normalizer" -version = "2.1.1" +version = "3.0.1" description = "The Real First Universal Charset Detector. 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hash = "sha256:4d3c92fac8f1118bb77a22181355e29c239cabfe2b9effdaa665c66b711136d7"}, + {file = "setuptools-66.0.0-py3-none-any.whl", hash = "sha256:a78d01d1e2c175c474884671dde039962c9d74c7223db7369771fcf6e29ceeab"}, + {file = "setuptools-66.0.0.tar.gz", hash = "sha256:bd6eb2d6722568de6d14b87c44a96fac54b2a45ff5e940e639979a3d1792adb6"}, ] [package.extras] @@ -1406,4 +1469,4 @@ test = [] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11" -content-hash = "b8f54bcf84483dd77925f9ad9b5ef7595e54d9447a75eae29dfc252fd4eff053" +content-hash = "fbdb9c6a8c3904bed53c016cc5d8311933c6e794a163e4a48d12e2ecae44085c" diff --git a/pyproject.toml b/pyproject.toml index 9c7d7d84d..e331c8a70 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,6 @@ packages = [ python = ">=3.8.0,<3.11" argcomplete = "^2.0.0" humanize = "^4.4.0" -numpy = "^1.24.1" pillow = "^9.4.0" pyyaml = ">=5.1" requests = "^2.28.1" @@ -31,6 +30,7 @@ jsonschema = "3.2.0" deprecation = "^2.1.0" pydantic = "^1.10.4" orjson = "^3.8.5" +numpy = "1.23.0" [tool.poetry.extras] From 4cf4585af2cabae855d32324e35f2d7a7a7ca178 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 14:28:42 +0000 Subject: [PATCH 12/49] Reducing test matrix, as 3.6 is very old --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 78a1bee91..b87cb4f55 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -30,7 +30,7 @@ jobs: timeout-minutes: 30 strategy: matrix: - python-version: [3.6, 3.7, 3.8, 3.9, "3.10"] + python-version: [3.7, 3.8, 3.9, "3.10"] steps: - uses: actions/checkout@v2 From 65b1a290a9f0efe9e4ca5eb212dae55e6b833d80 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 14:30:51 +0000 Subject: [PATCH 13/49] Setting more flexible numpy version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e331c8a70..7a3d0b3af 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,7 @@ jsonschema = "3.2.0" deprecation = "^2.1.0" pydantic = "^1.10.4" orjson = "^3.8.5" -numpy = "1.23.0" +numpy = "<=1.23.0" [tool.poetry.extras] From 2c39d1f34f3ba9f4ea8dc1fd7baa4295759b8ef5 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 14:40:07 +0000 Subject: [PATCH 14/49] Flows install using poetry --- .github/workflows/document.yml | 4 ++-- .github/workflows/tests.yml | 10 ++++------ 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/.github/workflows/document.yml b/.github/workflows/document.yml index 27da875a5..14eeefdbf 100644 --- a/.github/workflows/document.yml +++ b/.github/workflows/document.yml @@ -20,8 +20,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install setuptools wheel - pip install --editable ".[test,medical]" + pip install poetry + poetry install --extras "test ml medical dev" -G dev pip install torch torchvision pip install -U sphinx # Locking mistune version so m2r works. More info on issue: diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index b87cb4f55..ba5ba9a21 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -19,9 +19,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install wheel - pip install --upgrade setuptools - pip install --editable ".[test,ml,medical]" + pip install poetry + poetry install --extras "test ml medical dev" -G dev - name: Run tests run: pytest @@ -41,9 +40,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install wheel - pip install --upgrade setuptools - pip install --editable ".[test,ml,medical]" + pip install poetry + poetry install --extras "test ml medical dev" -G dev - name: Run tests run: pytest From d7b540f6733c71a419175974f0500995f756c40b Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 14:42:36 +0000 Subject: [PATCH 15/49] Corrected add syntax to install syntax in flows --- .github/workflows/document.yml | 2 +- .github/workflows/tests.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/document.yml b/.github/workflows/document.yml index 14eeefdbf..bdc60e0bc 100644 --- a/.github/workflows/document.yml +++ b/.github/workflows/document.yml @@ -21,7 +21,7 @@ jobs: run: | python -m pip install --upgrade pip pip install poetry - poetry install --extras "test ml medical dev" -G dev + poetry install --extras "test ml medical dev" --with dev pip install torch torchvision pip install -U sphinx # Locking mistune version so m2r works. More info on issue: diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index ba5ba9a21..c4c41ca6b 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -20,7 +20,7 @@ jobs: run: | python -m pip install --upgrade pip pip install poetry - poetry install --extras "test ml medical dev" -G dev + poetry install --extras "test ml medical dev" --with dev - name: Run tests run: pytest @@ -41,7 +41,7 @@ jobs: run: | python -m pip install --upgrade pip pip install poetry - poetry install --extras "test ml medical dev" -G dev + poetry install --extras "test ml medical dev" --with dev - name: Run tests run: pytest From 3589078b99638c21a4b5c87906e9d4351bd11958 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 14:46:53 +0000 Subject: [PATCH 16/49] Lock file --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 3d5aec262..ca61bba51 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1469,4 +1469,4 @@ test = [] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11" -content-hash = "fbdb9c6a8c3904bed53c016cc5d8311933c6e794a163e4a48d12e2ecae44085c" +content-hash = "cea7583ac769d587009a812b71aa1166f3a28d84219825da8dc6146bccaff7ce" From 92b4ae510c6414be4dac179e0481418fad70cdd8 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 15:01:21 +0000 Subject: [PATCH 17/49] Adding env invoke --- .github/workflows/document.yml | 1 + .github/workflows/tests.yml | 8 ++++++-- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/document.yml b/.github/workflows/document.yml index bdc60e0bc..e3c845428 100644 --- a/.github/workflows/document.yml +++ b/.github/workflows/document.yml @@ -22,6 +22,7 @@ jobs: python -m pip install --upgrade pip pip install poetry poetry install --extras "test ml medical dev" --with dev + poetry shell pip install torch torchvision pip install -U sphinx # Locking mistune version so m2r works. More info on issue: diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c4c41ca6b..6c9524f02 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -23,7 +23,9 @@ jobs: poetry install --extras "test ml medical dev" --with dev - name: Run tests - run: pytest + run: | + poetry shell + pytest windows: runs-on: windows-latest timeout-minutes: 30 @@ -44,4 +46,6 @@ jobs: poetry install --extras "test ml medical dev" --with dev - name: Run tests - run: pytest + run: | + poetry shell + pytest From 18019568405d0eec55b3c038eab64d826b90292f Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 15:31:26 +0000 Subject: [PATCH 18/49] Poetry run added --- .github/workflows/tests.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6c9524f02..6d94bcd37 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -24,8 +24,7 @@ jobs: - name: Run tests run: | - poetry shell - pytest + poetry run pytest windows: runs-on: windows-latest timeout-minutes: 30 @@ -47,5 +46,4 @@ jobs: - name: Run tests run: | - poetry shell - pytest + poetry run pytest From 374a28879222f46447705bde4d7ccf1631594a85 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 15:33:32 +0000 Subject: [PATCH 19/49] Add no interaction --- .github/workflows/tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6d94bcd37..f0a9571d4 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -20,7 +20,7 @@ jobs: run: | python -m pip install --upgrade pip pip install poetry - poetry install --extras "test ml medical dev" --with dev + poetry install --extras "test ml medical dev" --with dev --no-interaction - name: Run tests run: | @@ -42,7 +42,7 @@ jobs: run: | python -m pip install --upgrade pip pip install poetry - poetry install --extras "test ml medical dev" --with dev + poetry install --extras "test ml medical dev" --with dev --no-interaction - name: Run tests run: | From d1e7974a12fea45ae109baafc0283cdc880330cb Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 16:56:50 +0000 Subject: [PATCH 20/49] trying a different approach --- .github/workflows/tests.yml | 36 ++++++++++++++++++++++++------------ 1 file changed, 24 insertions(+), 12 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index f0a9571d4..94938d277 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -6,25 +6,37 @@ jobs: ubuntu: runs-on: ubuntu-latest timeout-minutes: 30 + env: + poetry_version: "1.3.2" strategy: matrix: python-version: [3.7, 3.8, 3.9, "3.10"] steps: - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + - uses: actions/setup-python@v2 with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install poetry - poetry install --extras "test ml medical dev" --with dev --no-interaction - - - name: Run tests - run: | - poetry run pytest + python-version: {{ matrix.python_version }} + - name: Cached Poetry Install + uses: actions/cache@v2 + with: + path: ~/.local + key: poetry-1.3.2-0 + - uses: snok/install-poetry@v1 + with: + version: 1.3.2 + virtualenvs-create: true + virtualenvs-in-project: true + - name: Cached install dependencies + id: cache-deps + uses: actions/cache@v2 + with: + path: .venv + key: pydeps-${{ hashFiles('**/poetry.lock') }} + - run: poetry install --no-interaction --no-root --all-extras + if: steps.cache-deps.outputs.cache-hit != 'true' + - run: poetry install --no-interaction + - run: poetry run pytest windows: runs-on: windows-latest timeout-minutes: 30 From b8782e32a95fa90a563b2b4388c5b4721ebfad16 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 17:02:50 +0000 Subject: [PATCH 21/49] YAML issues --- .github/workflows/tests.yml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 94938d277..e842a5660 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -6,28 +6,26 @@ jobs: ubuntu: runs-on: ubuntu-latest timeout-minutes: 30 - env: - poetry_version: "1.3.2" strategy: matrix: python-version: [3.7, 3.8, 3.9, "3.10"] - steps: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: python-version: {{ matrix.python_version }} - - name: Cached Poetry Install + - name: Cache Poetry Install uses: actions/cache@v2 with: path: ~/.local key: poetry-1.3.2-0 - - uses: snok/install-poetry@v1 + - name: Install Poetry + uses: snok/install-poetry@v1 with: version: 1.3.2 virtualenvs-create: true virtualenvs-in-project: true - - name: Cached install dependencies + - name: Install dependencies id: cache-deps uses: actions/cache@v2 with: @@ -35,8 +33,9 @@ jobs: key: pydeps-${{ hashFiles('**/poetry.lock') }} - run: poetry install --no-interaction --no-root --all-extras if: steps.cache-deps.outputs.cache-hit != 'true' - - run: poetry install --no-interaction - - run: poetry run pytest + - run: poetry install --no-interaction + - name: Run Tests + run: poetry run pytest windows: runs-on: windows-latest timeout-minutes: 30 From 11bd8e768d942cb8a72446467b661147229350e7 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 17:04:42 +0000 Subject: [PATCH 22/49] Fixed variable issue --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index e842a5660..7fedc2dcd 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -13,7 +13,7 @@ jobs: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 with: - python-version: {{ matrix.python_version }} + python-version: ${{ matrix.python_version }} - name: Cache Poetry Install uses: actions/cache@v2 with: From bfa3521fe7658f0054006bb2fff179b3c47e696b Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 17:18:33 +0000 Subject: [PATCH 23/49] Installed toml dependency --- poetry.lock | 14 +++++++++++++- pyproject.toml | 1 + 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index ca61bba51..e49683c85 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1392,6 +1392,18 @@ files = [ {file = "threadpoolctl-3.1.0.tar.gz", hash = "sha256:a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380"}, ] +[[package]] +name = "toml" +version = "0.10.2" +description = "Python Library for Tom's Obvious, Minimal Language" +category = "main" +optional = false +python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" +files = [ + {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"}, + {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"}, +] + [[package]] name = "tomli" version = "2.0.1" @@ -1469,4 +1481,4 @@ test = [] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11" -content-hash = "cea7583ac769d587009a812b71aa1166f3a28d84219825da8dc6146bccaff7ce" +content-hash = "6aff6348611a4b3183111b2c393c63a8882172917330fecc0425bd0b94a2956d" diff --git a/pyproject.toml b/pyproject.toml index 7a3d0b3af..a74138332 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,6 +31,7 @@ deprecation = "^2.1.0" pydantic = "^1.10.4" orjson = "^3.8.5" numpy = "<=1.23.0" +toml = "^0.10.2" [tool.poetry.extras] From 5221f3bae8ce610202cebd37a69f97493bdaabc3 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 17:20:10 +0000 Subject: [PATCH 24/49] Giving up on toml --- darwin/version/__init__.py | 15 +-------------- poetry.lock | 14 +------------- pyproject.toml | 1 - 3 files changed, 2 insertions(+), 28 deletions(-) diff --git a/darwin/version/__init__.py b/darwin/version/__init__.py index 9bf8efa15..686e10f8f 100644 --- a/darwin/version/__init__.py +++ b/darwin/version/__init__.py @@ -1,14 +1 @@ -from os.path import dirname -from pathlib import Path - -from toml import load - -version_path = Path(dirname(__file__)) / ".." / ".." / "pyproject.toml" - -pyproject = load(version_path.resolve()) -version = pyproject.get("tool", {}).get("poetry", {}).get("version") - -if version is None: - raise SystemExit("Project file doesn't contain a version") - -__version__ = version +__version__ = "0.8.7" diff --git a/poetry.lock b/poetry.lock index e49683c85..ca61bba51 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1392,18 +1392,6 @@ files = [ {file = "threadpoolctl-3.1.0.tar.gz", hash = "sha256:a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380"}, ] -[[package]] -name = "toml" -version = "0.10.2" -description = "Python Library for Tom's Obvious, Minimal Language" -category = "main" -optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" -files = [ - {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"}, - {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"}, -] - [[package]] name = "tomli" version = "2.0.1" @@ -1481,4 +1469,4 @@ test = [] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11" -content-hash = "6aff6348611a4b3183111b2c393c63a8882172917330fecc0425bd0b94a2956d" +content-hash = "cea7583ac769d587009a812b71aa1166f3a28d84219825da8dc6146bccaff7ce" diff --git a/pyproject.toml b/pyproject.toml index a74138332..7a3d0b3af 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,6 @@ deprecation = "^2.1.0" pydantic = "^1.10.4" orjson = "^3.8.5" numpy = "<=1.23.0" -toml = "^0.10.2" [tool.poetry.extras] From 2a1b42d7944d8732458f1cd0b3f4a4f6e448a153 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 17:24:26 +0000 Subject: [PATCH 25/49] Tweak to try different version of command --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 7fedc2dcd..69a9ac912 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -33,7 +33,7 @@ jobs: key: pydeps-${{ hashFiles('**/poetry.lock') }} - run: poetry install --no-interaction --no-root --all-extras if: steps.cache-deps.outputs.cache-hit != 'true' - - run: poetry install --no-interaction + - run: poetry install --no-interaction --all-extras - name: Run Tests run: poetry run pytest windows: From 6f19fb587d29b6f925749d693e717de4e7a196b3 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 17:29:22 +0000 Subject: [PATCH 26/49] One more go --- .github/workflows/pythonpublish_sdist.yml | 2 +- .github/workflows/tests.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pythonpublish_sdist.yml b/.github/workflows/pythonpublish_sdist.yml index a2da422bb..2419ad317 100644 --- a/.github/workflows/pythonpublish_sdist.yml +++ b/.github/workflows/pythonpublish_sdist.yml @@ -18,7 +18,7 @@ jobs: run: | python -m pip install --upgrade pip pip install poetry - poetry install --extras "test ml medical dev" -G dev + poetry install --extras "test ml medical dev" --with dev poetry build - name: Publish env: diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 69a9ac912..84a952d5b 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -31,9 +31,9 @@ jobs: with: path: .venv key: pydeps-${{ hashFiles('**/poetry.lock') }} - - run: poetry install --no-interaction --no-root --all-extras + - run: poetry install --no-interaction --no-root --extras "ml medical test dev" --with dev if: steps.cache-deps.outputs.cache-hit != 'true' - - run: poetry install --no-interaction --all-extras + - run: poetry install --no-interaction --extras "ml medical test dev" --with dev - name: Run Tests run: poetry run pytest windows: From 8d650e23244695178b4c1ec2ea2be3a05ca8537e Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 22:40:19 +0000 Subject: [PATCH 27/49] New version of the CI/CD flow --- .github/workflows/tests.yml | 128 ++++++++++++++++++++++-------------- 1 file changed, 78 insertions(+), 50 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 84a952d5b..a98668f8d 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,60 +1,88 @@ -name: Testing - -on: [push] +# CI/CD Flow jobs: - ubuntu: - runs-on: ubuntu-latest - timeout-minutes: 30 + tests: strategy: + fail-fast: false matrix: - python-version: [3.7, 3.8, 3.9, "3.10"] + python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11"] + poetry-version: ["1.13.0", "1.32.0"] + os: [ubuntu-latest, windows-latest] + runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python_version }} - - name: Cache Poetry Install - uses: actions/cache@v2 + name: Setup Python ${{ matrix.python-version }} on ${{ matrix.os }} using Poetry ${{ matrix.poetry-version }} + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 with: - path: ~/.local - key: poetry-1.3.2-0 - - name: Install Poetry - uses: snok/install-poetry@v1 - with: - version: 1.3.2 - virtualenvs-create: true - virtualenvs-in-project: true - - name: Install dependencies - id: cache-deps - uses: actions/cache@v2 + python-version: ${{ matrix.python-version }} + - name: Run image + uses: abatilo/actions-poetry@v2 with: - path: .venv - key: pydeps-${{ hashFiles('**/poetry.lock') }} - - run: poetry install --no-interaction --no-root --extras "ml medical test dev" --with dev - if: steps.cache-deps.outputs.cache-hit != 'true' - - run: poetry install --no-interaction --extras "ml medical test dev" --with dev - - name: Run Tests + poetry-version: ${{ matrix.poetry-version }} + - name: Install Dependencies' + run: poetry install --no-root --no-interaction --extras "ml medical test dev" --with dev + - name: Run tests run: poetry run pytest - windows: - runs-on: windows-latest - timeout-minutes: 30 - strategy: - matrix: - python-version: [3.7, 3.8, 3.9, "3.10"] + + - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install poetry - poetry install --extras "test ml medical dev" --with dev --no-interaction +# name: Testing - - name: Run tests - run: | - poetry run pytest +# on: [push] + +# jobs: +# ubuntu: +# runs-on: ubuntu-latest +# timeout-minutes: 30 +# strategy: +# matrix: +# python-version: [3.7, 3.8, 3.9, "3.10"] +# steps: +# - uses: actions/checkout@v2 +# - uses: actions/setup-python@v2 +# with: +# python-version: ${{ matrix.python_version }} +# - name: Cache Poetry Install +# uses: actions/cache@v2 +# with: +# path: ~/.local +# key: poetry-1.3.2-0 +# - name: Install Poetry +# uses: snok/install-poetry@v1 +# with: +# version: 1.3.2 +# virtualenvs-create: true +# virtualenvs-in-project: true +# - name: Install dependencies +# id: cache-deps +# uses: actions/cache@v2 +# with: +# path: .venv +# key: pydeps-${{ hashFiles('**/poetry.lock') }} +# - run: poetry install --no-interaction --no-root --extras "ml medical test dev" --with dev +# if: steps.cache-deps.outputs.cache-hit != 'true' +# - run: poetry install --no-interaction --extras "ml medical test dev" --with dev +# - name: Run Tests +# run: poetry run pytest +# windows: +# runs-on: windows-latest +# timeout-minutes: 30 +# strategy: +# matrix: +# python-version: [3.7, 3.8, 3.9, "3.10"] + +# steps: +# - uses: actions/checkout@v2 +# - name: Set up Python ${{ matrix.python-version }} +# uses: actions/setup-python@v2 +# with: +# python-version: ${{ matrix.python-version }} +# - name: Install dependencies +# run: | +# python -m pip install --upgrade pip +# pip install poetry +# poetry install --extras "test ml medical dev" --with dev --no-interaction + +# - name: Run tests +# run: | +# poetry run pytest From ebd05e4bc8c7ff62906ec5c59cda00828af48662 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 22:41:57 +0000 Subject: [PATCH 28/49] Added in name and action --- .github/workflows/tests.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index a98668f8d..6b72fe1bc 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,5 +1,9 @@ # CI/CD Flow +name: Testing + +on: [pull-request, merge] + jobs: tests: strategy: From 51dc3491d83b7051505987d8b2acc07b208e5ee8 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 22:46:15 +0000 Subject: [PATCH 29/49] Change trigger --- .github/workflows/tests.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6b72fe1bc..ca0d03798 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -2,7 +2,10 @@ name: Testing -on: [pull-request, merge] +on: + pull-request: + branches: + - master jobs: tests: From 2a42127058e0258e45fb4970ced559c39ee8e683 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 22:54:37 +0000 Subject: [PATCH 30/49] Trying a new action --- .github/workflows/tests.yml | 25 ++++++++++--------------- 1 file changed, 10 insertions(+), 15 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index ca0d03798..bff6e6346 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,35 +1,30 @@ -# CI/CD Flow - -name: Testing - +name: CI on: - pull-request: + push: branches: - master + pull_request: jobs: - tests: + ci: strategy: fail-fast: false matrix: - python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11"] - poetry-version: ["1.13.0", "1.32.0"] + python-version: ["3.8", "3.9", "3.10", "3.11"] + poetry-version: ["1.2.2", "1.3.1"] os: [ubuntu-latest, windows-latest] runs-on: ${{ matrix.os }} steps: - name: Setup Python ${{ matrix.python-version }} on ${{ matrix.os }} using Poetry ${{ matrix.poetry-version }} - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v2 + - uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - name: Run image uses: abatilo/actions-poetry@v2 with: poetry-version: ${{ matrix.poetry-version }} - - name: Install Dependencies' - run: poetry install --no-root --no-interaction --extras "ml medical test dev" --with dev - - name: Run tests - run: poetry run pytest + - name: View poetry --help + run: poetry --help From fb5306df1dd31a63fa0bd936d0b2258c50a370bb Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 22:57:47 +0000 Subject: [PATCH 31/49] Added install and tests --- .github/workflows/tests.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index bff6e6346..ee0c395c9 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -23,8 +23,10 @@ jobs: uses: abatilo/actions-poetry@v2 with: poetry-version: ${{ matrix.poetry-version }} - - name: View poetry --help - run: poetry --help + - name: Install dependencies + run: poetry install --extras "ml medical test dev" --with dev + - name: Run Tests + run: poetry run pytest From ee07f7da2aad0d1190b10d3d331e22767a055662 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 22:59:55 +0000 Subject: [PATCH 32/49] Minor semantic changes --- .github/workflows/tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index ee0c395c9..791929dd1 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,4 +1,4 @@ -name: CI +name: Testing on: push: branches: @@ -19,7 +19,7 @@ jobs: - uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - - name: Run image + - name: Setup Poetry uses: abatilo/actions-poetry@v2 with: poetry-version: ${{ matrix.poetry-version }} From 1fcbc25af8ad145c053e180f3e6167cfb440a6b7 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 23:04:09 +0000 Subject: [PATCH 33/49] Still not installing pytest, trying a different approach --- .github/workflows/tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 791929dd1..663883709 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -24,9 +24,9 @@ jobs: with: poetry-version: ${{ matrix.poetry-version }} - name: Install dependencies - run: poetry install --extras "ml medical test dev" --with dev + run: poetry install --no-interaction --no-root --extras "ml medical test dev" --with dev - name: Run Tests - run: poetry run pytest + run: pytest From 3f9b997920ec36abc0bdb59336a0bcd72cf9031e Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Mon, 16 Jan 2023 23:07:21 +0000 Subject: [PATCH 34/49] Tweaking install line --- .github/workflows/tests.yml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 663883709..a51ba1d67 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -24,7 +24,7 @@ jobs: with: poetry-version: ${{ matrix.poetry-version }} - name: Install dependencies - run: poetry install --no-interaction --no-root --extras "ml medical test dev" --with dev + run: poetry install --no-interaction --no-root --extras "ml medical test dev" - name: Run Tests run: pytest diff --git a/pyproject.toml b/pyproject.toml index 7a3d0b3af..7f31269e7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,7 +35,7 @@ numpy = "<=1.23.0" [tool.poetry.extras] test = ["responses", "pytest", "pytest-describe", "scikit-learn"] -dev = ["black", "flake8", "isort", "mypy", "responses", "pytest", "pytest-describe", "scikit-learn"] +dev = ["black", "flake8", "isort", "mypy"] ml = ["scikit-learn", "torch", "torchvision"] medical = ["nibabel", "connected-components-3d"] From 1fbf144a65155294092177ba3b5be0af86577862 Mon Sep 17 00:00:00 2001 From: Owen Date: Mon, 16 Jan 2023 23:20:42 +0000 Subject: [PATCH 35/49] Update lock file --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index ca61bba51..5d0e6fc8a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1469,4 +1469,4 @@ test = [] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11" -content-hash = "cea7583ac769d587009a812b71aa1166f3a28d84219825da8dc6146bccaff7ce" +content-hash = "0792fa84b254c302b9bc58d79ac82c7b82b1134e12fcc3d604872af540a9e34a" From 94d5e955dd6ce18d0f4d3f3e75ed17c7aeaa9235 Mon Sep 17 00:00:00 2001 From: Owen Date: Mon, 16 Jan 2023 23:22:50 +0000 Subject: [PATCH 36/49] Changing to run pytest --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index a51ba1d67..89e4ed64f 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -26,7 +26,7 @@ jobs: - name: Install dependencies run: poetry install --no-interaction --no-root --extras "ml medical test dev" - name: Run Tests - run: pytest + run: poetry run pytest From 81a750f160cb957a8b730cac3d3a2f353a9e2bd1 Mon Sep 17 00:00:00 2001 From: Owen Date: Mon, 16 Jan 2023 23:24:38 +0000 Subject: [PATCH 37/49] Pytest maybe doesn't work with 3.8 anymore --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 89e4ed64f..378fa9d05 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -10,7 +10,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11"] poetry-version: ["1.2.2", "1.3.1"] os: [ubuntu-latest, windows-latest] runs-on: ${{ matrix.os }} From f937e3160338aef4e22e85f5c14c59a9333fe140 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Tue, 17 Jan 2023 10:45:54 +0000 Subject: [PATCH 38/49] Fixed Dependency issue --- .github/workflows/tests.yml | 2 +- pyproject.toml | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 378fa9d05..89e4ed64f 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -10,7 +10,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.8", "3.9", "3.10", "3.11"] poetry-version: ["1.2.2", "1.3.1"] os: [ubuntu-latest, windows-latest] runs-on: ${{ matrix.os }} diff --git a/pyproject.toml b/pyproject.toml index 7f31269e7..111b2c6b3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,12 +45,12 @@ medical = ["nibabel", "connected-components-3d"] black = {markers = "python_version > \"3.9\"", version = "^22.12.0"} isort = {markers = "python_version > \"3.9\"", version = "^5.11.4"} mypy = {markers = "python_version > \"3.9\"", version = "^0.991"} -response = {markers = "python_version > \"3.9\"", version = "^0.5.0"} -pytest = {markers = "python_version > \"3.9\"", version = "^7.2.0"} -pytest-describe = {markers = "python_version > \"3.9\"", version = "^2.0.1"} -scikit-learn = {markers = "python_version > \"3.9\"", version ="^1.2.0"} -flake8 = {markers = "python_version > \"3.9\"", version = "^6.0.0"} -flake8-pyproject = {markers = "python_version > \"3.9\"", version = "^1.2.2"} +response = {markers = "python_version > \"3.8\"", version = "^0.5.0"} +pytest = {markers = "python_version > \"3.8\"", version = "^7.2.0"} +pytest-describe = {markers = "python_version > \"3.8\"", version = "^2.0.1"} +scikit-learn = {markers = "python_version > \"3.8\"", version ="^1.2.0"} +flake8 = {markers = "python_version > \"3.8\"", version = "^6.0.0"} +flake8-pyproject = {markers = "python_version > \"3.8\"", version = "^1.2.2"} debugpy = {markers = "python_version > \"3.9\"", version = "^1.6.5"} [tool.poetry.scripts] From ac430b675a1fd325a3d58ebf3a0dca2895b85384 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Tue, 17 Jan 2023 10:50:04 +0000 Subject: [PATCH 39/49] Added lock file --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 5d0e6fc8a..21121bc50 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1469,4 +1469,4 @@ test = [] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11" -content-hash = "0792fa84b254c302b9bc58d79ac82c7b82b1134e12fcc3d604872af540a9e34a" +content-hash = "b6919cf80a80f0b431baefdd31a1c3e3e9650244cac2a832be9985c13f2706c9" From 5da45f2b0357ddc4e03aa62139492145e152ec2d Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Tue, 17 Jan 2023 10:54:10 +0000 Subject: [PATCH 40/49] Issue with flake8 --- poetry.lock | 3 ++- pyproject.toml | 20 ++++++++++---------- 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/poetry.lock b/poetry.lock index 21121bc50..1cc0c9cd6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -62,6 +62,7 @@ mypy-extensions = ">=0.4.3" pathspec = ">=0.9.0" platformdirs = ">=2" tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""} +typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""} [package.extras] colorama = ["colorama (>=0.4.3)"] @@ -1469,4 +1470,4 @@ test = [] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11" -content-hash = "b6919cf80a80f0b431baefdd31a1c3e3e9650244cac2a832be9985c13f2706c9" +content-hash = "99dff465106b102353726b358e04cc340af071e998c3a0ff935b7499cfd0c4ed" diff --git a/pyproject.toml b/pyproject.toml index 111b2c6b3..3c2830efe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,16 +42,16 @@ medical = ["nibabel", "connected-components-3d"] [tool.poetry.group] [tool.poetry.group.dev.dependencies] -black = {markers = "python_version > \"3.9\"", version = "^22.12.0"} -isort = {markers = "python_version > \"3.9\"", version = "^5.11.4"} -mypy = {markers = "python_version > \"3.9\"", version = "^0.991"} -response = {markers = "python_version > \"3.8\"", version = "^0.5.0"} -pytest = {markers = "python_version > \"3.8\"", version = "^7.2.0"} -pytest-describe = {markers = "python_version > \"3.8\"", version = "^2.0.1"} -scikit-learn = {markers = "python_version > \"3.8\"", version ="^1.2.0"} -flake8 = {markers = "python_version > \"3.8\"", version = "^6.0.0"} -flake8-pyproject = {markers = "python_version > \"3.8\"", version = "^1.2.2"} -debugpy = {markers = "python_version > \"3.9\"", version = "^1.6.5"} +black = {markers = "python_version >= \"3.9\"", version = "^22.12.0"} +isort = {markers = "python_version >= \"3.9\"", version = "^5.11.4"} +mypy = {markers = "python_version >= \"3.9\"", version = "^0.991"} +response = {markers = "python_version >= \"3.8\"", version = "^0.5.0"} +pytest = {markers = "python_version >= \"3.8\"", version = "^7.2.0"} +pytest-describe = {markers = "python_version >= \"3.8\"", version = "^2.0.1"} +scikit-learn = {markers = "python_version >= \"3.8\"", version ="^1.2.0"} +flake8 = {markers = "python_version >= \"3.8.1,<3.11\"", version = "^6.0.0"} +flake8-pyproject = {markers = "python_version >= \"3.8\"", version = "^1.2.2"} +debugpy = {markers = "python_version >= \"3.9\"", version = "^1.6.5"} [tool.poetry.scripts] darwin = "darwin.cli:main" From 2ae0f41623a6f83be12908887023c5f347462fdd Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Tue, 17 Jan 2023 11:27:04 +0000 Subject: [PATCH 41/49] Upgrade to gitflow, not going to fix the pytest modules just yet --- .github/workflows/tests.yml | 74 ++++--------------------------------- 1 file changed, 8 insertions(+), 66 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 89e4ed64f..44df839f7 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,4 +1,9 @@ name: Testing + +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + on: push: branches: @@ -11,7 +16,7 @@ jobs: fail-fast: false matrix: python-version: ["3.8", "3.9", "3.10", "3.11"] - poetry-version: ["1.2.2", "1.3.1"] + poetry-version: ["1.3.1"] os: [ubuntu-latest, windows-latest] runs-on: ${{ matrix.os }} steps: @@ -24,69 +29,6 @@ jobs: with: poetry-version: ${{ matrix.poetry-version }} - name: Install dependencies - run: poetry install --no-interaction --no-root --extras "ml medical test dev" + run: poetry install --no-interaction --no-root --extras "ml medical test dev" --with dev - name: Run Tests - run: poetry run pytest - - - -# name: Testing - -# on: [push] - -# jobs: -# ubuntu: -# runs-on: ubuntu-latest -# timeout-minutes: 30 -# strategy: -# matrix: -# python-version: [3.7, 3.8, 3.9, "3.10"] -# steps: -# - uses: actions/checkout@v2 -# - uses: actions/setup-python@v2 -# with: -# python-version: ${{ matrix.python_version }} -# - name: Cache Poetry Install -# uses: actions/cache@v2 -# with: -# path: ~/.local -# key: poetry-1.3.2-0 -# - name: Install Poetry -# uses: snok/install-poetry@v1 -# with: -# version: 1.3.2 -# virtualenvs-create: true -# virtualenvs-in-project: true -# - name: Install dependencies -# id: cache-deps -# uses: actions/cache@v2 -# with: -# path: .venv -# key: pydeps-${{ hashFiles('**/poetry.lock') }} -# - run: poetry install --no-interaction --no-root --extras "ml medical test dev" --with dev -# if: steps.cache-deps.outputs.cache-hit != 'true' -# - run: poetry install --no-interaction --extras "ml medical test dev" --with dev -# - name: Run Tests -# run: poetry run pytest -# windows: -# runs-on: windows-latest -# timeout-minutes: 30 -# strategy: -# matrix: -# python-version: [3.7, 3.8, 3.9, "3.10"] - -# steps: -# - uses: actions/checkout@v2 -# - name: Set up Python ${{ matrix.python-version }} -# uses: actions/setup-python@v2 -# with: -# python-version: ${{ matrix.python-version }} -# - name: Install dependencies -# run: | -# python -m pip install --upgrade pip -# pip install poetry -# poetry install --extras "test ml medical dev" --with dev --no-interaction - -# - name: Run tests -# run: | -# poetry run pytest + run: poetry run pytest \ No newline at end of file From a0b11b71a7fed53c367bba9c459681e735213cc5 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Tue, 17 Jan 2023 13:14:24 +0000 Subject: [PATCH 42/49] Resolved deps, test changes --- .github/workflows/tests.yml | 8 +- poetry.lock | 602 +++++++++++++++++------------------- pyproject.toml | 35 +-- 3 files changed, 306 insertions(+), 339 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 44df839f7..7e1432915 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -24,11 +24,15 @@ jobs: - uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} + run: pip install pip --upgrade - name: Setup Poetry uses: abatilo/actions-poetry@v2 with: poetry-version: ${{ matrix.poetry-version }} - name: Install dependencies - run: poetry install --no-interaction --no-root --extras "ml medical test dev" --with dev + run: | + poetry install --no-interaction --no-root --extras "ml medical test dev" --with dev + pip install . + pip install pytest pytest-describe - name: Run Tests - run: poetry run pytest \ No newline at end of file + run: pytest \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index 1cc0c9cd6..1ac397ca7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -38,7 +38,7 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy name = "black" version = 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00:00:00 2001 From: Owen Jones Date: Tue, 17 Jan 2023 13:33:18 +0000 Subject: [PATCH 44/49] Syntax issue in action --- .github/workflows/tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 1295906cf..62b84f71a 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -20,7 +20,7 @@ jobs: - uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - run: pip install pip --upgrade + - run: pip install pip --upgrade - name: Setup Poetry uses: abatilo/actions-poetry@v2 with: @@ -31,4 +31,4 @@ jobs: pip install . pip install pytest pytest-describe - name: Run Tests - run: pytest \ No newline at end of file + run: pytest From 6214a8e036603452ab5965fd4c2456a97c0b3d76 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Tue, 17 Jan 2023 13:46:22 +0000 Subject: [PATCH 45/49] Resolves all deps and should install and test --- .github/workflows/tests.yml | 2 +- poetry.lock | 96 ++++++++++++++++++++++++++++++++++++- pyproject.toml | 7 ++- 3 files changed, 102 insertions(+), 3 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 62b84f71a..2dc574786 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -27,7 +27,7 @@ jobs: poetry-version: ${{ matrix.poetry-version }} - name: Install dependencies run: | - poetry install --no-interaction --no-root --extras "ml medical test dev" --with dev + poetry install --no-interaction --no-root --all-extras -vvv pip install . pip install pytest pytest-describe - name: Run Tests diff --git a/poetry.lock b/poetry.lock index 1ac397ca7..e53e36afe 100644 --- a/poetry.lock +++ b/poetry.lock @@ -263,6 +263,73 @@ files = [ [package.dependencies] numpy = "*" +[[package]] +name = "coverage" +version = "7.0.5" +description = "Code coverage measurement for Python" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = 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+[[package]] +name = "pytest-cov" +version = "4.0.0" +description = "Pytest plugin for measuring coverage." +category = "main" +optional = false +python-versions = ">=3.6" +files = [ + {file = "pytest-cov-4.0.0.tar.gz", hash = "sha256:996b79efde6433cdbd0088872dbc5fb3ed7fe1578b68cdbba634f14bb8dd0470"}, + {file = "pytest_cov-4.0.0-py3-none-any.whl", hash = "sha256:2feb1b751d66a8bd934e5edfa2e961d11309dc37b73b0eabe73b5945fee20f6b"}, +] + +[package.dependencies] +coverage = {version = ">=5.2.1", extras = ["toml"]} +pytest = ">=4.6" + +[package.extras] +testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"] + [[package]] name = "pytest-describe" version = "2.0.1" @@ -1435,7 +1523,13 @@ files = [ [package.extras] test = ["pytest (>=3.0.0)"] +[extras] +dev = ["black", "isort", "flake8", "mypy", "debugpy", "responses", "pytest", "pytest-describe", "flake8-pyproject"] +medical = ["nibabel", "connected-components-3d"] +ml = ["torch", "torchvision", "scikit-learn"] +test = ["responses", "pytest", "pytest-describe", "flake8-pyproject"] + [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11" -content-hash = "eb8d53f1afea87dadaedb37b715e77bf4dd1b1c7aaa452f4a9ccaa4a7a75572f" +content-hash = "cc26a466075bd37d2ba502b085731862f201f72719b2e7c63141991fbea0f04d" diff --git a/pyproject.toml b/pyproject.toml index 919716865..44a615942 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,9 +44,14 @@ mypy = {version = "^0.991", extras = ["dev"]} responses = {version = "^0.22.0", extras = ["test", "dev"]} pytest = {version = "^7.2.1", extras = ["test", "dev"]} pytest-describe = {version = "^2.0.1", extras = ["test", "dev"]} -flake8-pyproject = {version = "^1.2.2", extras = ["test dev"], python = ">=3.8.1,<3.11"} +flake8-pyproject = {version = "^1.2.2", extras = ["test", "dev"], python = ">=3.8.1,<3.11"} debugpy = {version = "^1.6.5", extras = ["dev"]} +[tool.poetry.extras] +dev = ["black", "isort", "flake8", "mypy", "debugpy", "responses", "pytest", "pytest-describe", "flake8-pyproject"] +test = ["responses", "pytest", "pytest-describe", "flake8-pyproject"] +ml = ["torch", "torchvision", "scikit-learn"] +medical = ["nibabel", "connected-components-3d"] [tool.poetry.scripts] darwin = "darwin.cli:main" From 3ad9e9aea35c619aacb17038f5aa64bbffa57d26 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Tue, 17 Jan 2023 13:54:31 +0000 Subject: [PATCH 46/49] Install local module with all deps --- .github/workflows/document.yml | 10 ++++++---- .github/workflows/tests.yml | 8 +++++++- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/.github/workflows/document.yml b/.github/workflows/document.yml index e3c845428..4bd1daf08 100644 --- a/.github/workflows/document.yml +++ b/.github/workflows/document.yml @@ -2,7 +2,7 @@ name: Documentation on: push: - branches: ['master'] + branches: ["master"] workflow_dispatch: jobs: @@ -21,8 +21,10 @@ jobs: run: | python -m pip install --upgrade pip pip install poetry - poetry install --extras "test ml medical dev" --with dev - poetry shell + poetry install --all-extras --no-interaction --no-root + pip install wheel + pip install --upgrade setuptools + pip install --editable ".[test,ml,medical,dev]" pip install torch torchvision pip install -U sphinx # Locking mistune version so m2r works. More info on issue: @@ -36,7 +38,7 @@ jobs: m2r README.md mv README.rst source/ - name: Generate new docs - env: + env: PYTHONPATH: "." run: | rm -rf docs/* diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 2dc574786..6b54a95f7 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -6,6 +6,10 @@ on: - master pull_request: +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + jobs: ci: strategy: @@ -28,7 +32,9 @@ jobs: - name: Install dependencies run: | poetry install --no-interaction --no-root --all-extras -vvv - pip install . + pip install wheel + pip install --upgrade setuptools + pip install --editable ".[test,ml,medical,dev]" pip install pytest pytest-describe - name: Run Tests run: pytest From 00c5750f7cdf9450f61c4b420b14be55cea326b3 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Tue, 17 Jan 2023 14:01:40 +0000 Subject: [PATCH 47/49] Removed 3.11 as we don't technically support it yet --- .github/workflows/tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 6b54a95f7..5c53d47ff 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -15,7 +15,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10", "3.11"] + python-version: ["3.8", "3.9", "3.10"] poetry-version: ["1.3.1"] os: [ubuntu-latest, windows-latest] runs-on: ${{ matrix.os }} From 503a82a23b9eca99dcf110e19ea68131704129c8 Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Tue, 17 Jan 2023 14:09:18 +0000 Subject: [PATCH 48/49] Updated the deployment technique --- .github/workflows/pythonpublish_sdist.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pythonpublish_sdist.yml b/.github/workflows/pythonpublish_sdist.yml index 2419ad317..f0cdbc91f 100644 --- a/.github/workflows/pythonpublish_sdist.yml +++ b/.github/workflows/pythonpublish_sdist.yml @@ -14,11 +14,14 @@ jobs: uses: actions/setup-python@v2 with: python-version: "3.x" + - run: pip install pip --upgrade + - name: Setup Poetry + uses: abatilo/actions-poetry@v2 + with: + poetry-version: "1.3.1" - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install poetry - poetry install --extras "test ml medical dev" --with dev + poetry install --no-interaction --no-root --all-extras -vvv poetry build - name: Publish env: From 21cbf8c7d58d97df9438fd3f9ce6c4346e286d9d Mon Sep 17 00:00:00 2001 From: Owen Jones Date: Thu, 26 Jan 2023 15:24:36 +0000 Subject: [PATCH 49/49] Incorporated JSONSchema update from other branch --- poetry.lock | 79 ++++++++++++++++++++++++++++++++++++-------------- pyproject.toml | 2 +- 2 files changed, 58 insertions(+), 23 deletions(-) diff --git a/poetry.lock b/poetry.lock index e53e36afe..44ebe03f3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -452,6 +452,25 @@ files = [ {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"}, ] +[[package]] +name = "importlib-resources" +version = "5.10.2" +description = "Read resources from Python packages" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "importlib_resources-5.10.2-py3-none-any.whl", hash = "sha256:7d543798b0beca10b6a01ac7cafda9f822c54db9e8376a6bf57e0cbd74d486b6"}, + {file = "importlib_resources-5.10.2.tar.gz", hash = "sha256:e4a96c8cc0339647ff9a5e0550d9f276fc5a01ffa276012b58ec108cfd7b8484"}, +] + +[package.dependencies] +zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] + [[package]] name = "iniconfig" version = "2.0.0" @@ -496,25 +515,25 @@ files = [ [[package]] name = "jsonschema" -version = "3.2.0" +version = "4.17.3" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7" files = [ - {file = "jsonschema-3.2.0-py2.py3-none-any.whl", hash = "sha256:4e5b3cf8216f577bee9ce139cbe72eca3ea4f292ec60928ff24758ce626cd163"}, - {file = "jsonschema-3.2.0.tar.gz", hash = "sha256:c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a"}, + {file = "jsonschema-4.17.3-py3-none-any.whl", hash = "sha256:a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6"}, + {file = "jsonschema-4.17.3.tar.gz", hash = "sha256:0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d"}, ] [package.dependencies] attrs = ">=17.4.0" -pyrsistent = ">=0.14.0" -setuptools = "*" -six = ">=1.11.0" +importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""} +pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""} +pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2" [package.extras] -format = ["idna", "jsonpointer (>1.13)", "rfc3987", "strict-rfc3339", "webcolors"] -format-nongpl = ["idna", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "webcolors"] +format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] +format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] [[package]] name = "mccabe" @@ -881,6 +900,18 @@ files = [ docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"] tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] +[[package]] +name = "pkgutil-resolve-name" +version = "1.3.10" +description = "Resolve a name to an object." +category = "main" +optional = false +python-versions = ">=3.6" +files = [ + {file = "pkgutil_resolve_name-1.3.10-py3-none-any.whl", hash = "sha256:ca27cc078d25c5ad71a9de0a7a330146c4e014c2462d9af19c6b828280649c5e"}, + {file = "pkgutil_resolve_name-1.3.10.tar.gz", hash = "sha256:357d6c9e6a755653cfd78893817c0853af365dd51ec97f3d358a819373bbd174"}, +] + [[package]] name = "platformdirs" version = "2.6.2" @@ -1312,18 +1343,6 @@ docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-g testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] -[[package]] -name = "six" -version = "1.16.0" -description = "Python 2 and 3 compatibility utilities" -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" -files = [ - {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"}, - {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"}, -] - [[package]] name = "threadpoolctl" version = "3.1.0" @@ -1523,6 +1542,22 @@ files = [ [package.extras] test = ["pytest (>=3.0.0)"] +[[package]] +name = "zipp" +version = "3.11.0" +description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "zipp-3.11.0-py3-none-any.whl", hash = "sha256:83a28fcb75844b5c0cdaf5aa4003c2d728c77e05f5aeabe8e95e56727005fbaa"}, + {file = "zipp-3.11.0.tar.gz", hash = "sha256:a7a22e05929290a67401440b39690ae6563279bced5f314609d9d03798f56766"}, +] + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] +testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] + [extras] dev = ["black", "isort", "flake8", "mypy", "debugpy", "responses", "pytest", "pytest-describe", "flake8-pyproject"] medical = ["nibabel", "connected-components-3d"] @@ -1532,4 +1567,4 @@ test = ["responses", "pytest", "pytest-describe", "flake8-pyproject"] [metadata] lock-version = "2.0" python-versions = ">=3.8.0,<3.11" -content-hash = "cc26a466075bd37d2ba502b085731862f201f72719b2e7c63141991fbea0f04d" +content-hash = "587fc718d0167387492c284bdead72438d179012e07ef760b91391d58687f97d" diff --git a/pyproject.toml b/pyproject.toml index 44a615942..b55de0ec6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,7 +26,7 @@ requests = "^2.28.1" rich = "^13.0.1" dataclasses = {markers = "python_version < \"3.7\"", version = "^0.8"} upolygon = "0.1.8" -jsonschema = "3.2.0" +jsonschema = ">=4.0.0" deprecation = "^2.1.0" pydantic = "^1.10.4" orjson = "^3.8.5"