From 3b41a3d6c89f19a9025de1d148cdf99ff36255b7 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:03:23 +0100 Subject: [PATCH 01/11] added matrix python --- .github/workflows/tests.yml | 21 +++++++++ docs/examples.md | 5 +-- mkdocs.yml | 5 +-- poetry.lock | 86 ++++++------------------------------- pyproject.toml | 1 + 5 files changed, 38 insertions(+), 80 deletions(-) create mode 100644 .github/workflows/tests.yml diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 0000000..7cf955d --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,21 @@ +name: Python package + +on: [push] + +jobs: + build: + + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest, macos-latest, windows-latest] + python-version: ["3.9", "3.10", "3.11", "pypy3.9", "pypy3.10"] + steps: + - uses: actions/checkout@v4 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + # You can test your matrix by printing the current Python version + - name: Display Python version + run: python -c "import sys; print(sys.version)" \ No newline at end of file diff --git a/docs/examples.md b/docs/examples.md index 9777a39..0e727b8 100644 --- a/docs/examples.md +++ b/docs/examples.md @@ -1,6 +1,3 @@ # Examples -This is an example of how to use the Spectromax... - -::: MTPHandler.core.plate.Plate - handler: python \ No newline at end of file +This is an example of how to use the Spectromax. \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 114a097..3976330 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -51,7 +51,4 @@ markdown_extensions: emoji_generator: !!python/name:material.extensions.emoji.to_svg - def_list - pymdownx.tasklist: - custom_checkbox: true - - admonition - - codehilite - - mkautodoc \ No newline at end of file + custom_checkbox: true \ No newline at end of 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(==1.4.1)", "types-Pillow"] -test = ["Pillow", "contourpy[test-no-images]", "matplotlib"] -test-no-images = ["pytest", "pytest-cov", "wurlitzer"] - [[package]] name = "contourpy" version = "1.2.0" @@ -1284,6 +1213,19 @@ files = [ {file = "mergedeep-1.3.4.tar.gz", hash = "sha256:0096d52e9dad9939c3d975a774666af186eda617e6ca84df4c94dec30004f2a8"}, ] +[[package]] +name = "mkautodoc" +version = "0.2.0" +description = "AutoDoc for MarkDown" +optional = false +python-versions = ">=3.6" +files = [ + {file = "mkautodoc-0.2.0.tar.gz", hash = "sha256:b6e0c89804ba39d453ce5795eb040e5615756f90438ac04f47e97893a86a10cd"}, +] + +[package.dependencies] +Markdown = "*" + [[package]] name = "mkdocs" version = "1.5.3" @@ -2644,4 +2586,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "599ad939b8382f1057c804466e3cad63f30f5f96994c4fdb17ee4cf8df45b5d3" +content-hash = "68f1c4df92318c80cb5a71f917b2ffddbb46666a04cfb55f21c6a012b94f9c36" diff --git a/pyproject.toml b/pyproject.toml index c20b96e..9e7e843 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,6 +22,7 @@ openpyxl = "^3.1.2" [tool.poetry.group.dev.dependencies] mkdocs-material = "^9.5.7" +mkautodoc = "^0.2.0" [build-system] requires = ["poetry-core"] From 374f64a8f67ecc6e4cca72c933558484a424f1a9 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:18:43 +0100 Subject: [PATCH 02/11] -.- --- .github/workflows/tests.yml | 94 ++++++++++++++++++++++++++++++++----- poetry.lock | 64 ++++++++++++++++++++++++- pyproject.toml | 1 + 3 files changed, 145 insertions(+), 14 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 7cf955d..9b1fc9c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,21 +1,89 @@ -name: Python package +name: test -on: [push] +on: pull_request jobs: - build: - - runs-on: ${{ matrix.os }} + linting: + runs-on: ubuntu-latest + steps: + #---------------------------------------------- + # check-out repo and set-up python + #---------------------------------------------- + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + #---------------------------------------------- + # load pip cache if cache exists + #---------------------------------------------- + - uses: actions/cache@v3 + with: + path: ~/.cache/pip + key: ${{ runner.os }}-pip + restore-keys: ${{ runner.os }}-pip + #---------------------------------------------- + # install and run linters + #---------------------------------------------- + - run: python -m pip install black flake8 isort + - run: | + flake8 . + black . --check + isort . + test: + needs: linting strategy: + fail-fast: true matrix: - os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.9", "3.10", "3.11", "pypy3.9", "pypy3.10"] + os: [ "ubuntu-latest", "macos-latest" ] + python-version: [ "3.9", "3.10", "3.11", "3.12" ] + django-version: [ "4", "5" ] + runs-on: ${{ matrix.os }} steps: - - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + #---------------------------------------------- + # check-out repo and set-up python + #---------------------------------------------- + - name: Check out repository + uses: actions/checkout@v4 + - name: Set up python ${{ matrix.python-version }} + id: setup-python + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - # You can test your matrix by printing the current Python version - - name: Display Python version - run: python -c "import sys; print(sys.version)" \ No newline at end of file + #---------------------------------------------- + # ----- install & configure poetry ----- + #---------------------------------------------- + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: true + virtualenvs-in-project: true + #---------------------------------------------- + # load cached venv if cache exists + #---------------------------------------------- + - name: Load cached venv + id: cached-poetry-dependencies + uses: actions/cache@v3 + with: + path: .venv + key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} + #---------------------------------------------- + # install dependencies if cache does not exist + #---------------------------------------------- + - name: Install dependencies + if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' + run: poetry install --no-interaction --no-root + #---------------------------------------------- + # install your root project, if required + #---------------------------------------------- + - name: Install library + run: poetry install --no-interaction + #---------------------------------------------- + # add matrix specifics and run test suite + #---------------------------------------------- + - name: Install django ${{ matrix.django-version }} + run: | + source .venv/bin/activate + pip install "Django==${{ matrix.django-version }}" + - name: Run tests + run: | + source .venv/bin/activate + pytest tests/ + coverage report \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index b458b41..3c9bee5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -508,6 +508,20 @@ files = [ {file = "et_xmlfile-1.1.0.tar.gz", hash = "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c"}, ] +[[package]] +name = "exceptiongroup" +version = "1.2.0" +description = "Backport of PEP 654 (exception groups)" +optional = false +python-versions = ">=3.7" +files = [ + {file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14"}, + {file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"}, +] + +[package.extras] +test = ["pytest (>=6)"] + [[package]] name = "fastjsonschema" version = "2.18.1" @@ -704,6 +718,17 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff", "zipp (>=3.17)"] +[[package]] +name = "iniconfig" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" +optional = false +python-versions = ">=3.7" +files = [ + {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"}, + {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, +] + [[package]] name = "jinja2" version = "3.1.2" @@ -1665,6 +1690,21 @@ files = [ packaging = "*" tenacity = ">=6.2.0" +[[package]] +name = "pluggy" +version = "1.4.0" +description = "plugin and hook calling mechanisms for python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "pluggy-1.4.0-py3-none-any.whl", hash = "sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981"}, + {file = "pluggy-1.4.0.tar.gz", hash = "sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be"}, +] + +[package.extras] +dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] + [[package]] name = "pydantic" version = "1.8.2" @@ -1788,6 +1828,28 @@ files = [ [package.extras] diagrams = ["jinja2", "railroad-diagrams"] +[[package]] +name = "pytest" +version = "8.0.0" +description = "pytest: simple powerful testing with Python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "pytest-8.0.0-py3-none-any.whl", hash = "sha256:50fb9cbe836c3f20f0dfa99c565201fb75dc54c8d76373cd1bde06b06657bdb6"}, + {file = "pytest-8.0.0.tar.gz", hash = "sha256:249b1b0864530ba251b7438274c4d251c58d868edaaec8762893ad4a0d71c36c"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "sys_platform == \"win32\""} +exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} +iniconfig = "*" +packaging = "*" +pluggy = ">=1.3.0,<2.0" +tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} + +[package.extras] +testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] + [[package]] name = "python-dateutil" version = "2.8.2" @@ -2586,4 +2648,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "68f1c4df92318c80cb5a71f917b2ffddbb46666a04cfb55f21c6a012b94f9c36" +content-hash = "4d7f88bb8dfd9447b5b331edce631a678b45ed8f8abb8e29cfef4ee05e2af438" diff --git a/pyproject.toml b/pyproject.toml index 9e7e843..415206f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,6 +23,7 @@ openpyxl = "^3.1.2" [tool.poetry.group.dev.dependencies] mkdocs-material = "^9.5.7" mkautodoc = "^0.2.0" +pytest = "^8.0.0" [build-system] requires = ["poetry-core"] From ccd0ea15c48f48da1c648ae63ac6efaece7049c2 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:19:46 +0100 Subject: [PATCH 03/11] -.- --- .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 9b1fc9c..419da68 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,6 +1,6 @@ name: test -on: pull_request +on: push jobs: linting: From ca753bbfba63d6dc028372ef79e51fc637160162 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:20:50 +0100 Subject: [PATCH 04/11] -.- --- .github/workflows/tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 419da68..cc0e48f 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -23,10 +23,10 @@ jobs: # install and run linters #---------------------------------------------- - run: python -m pip install black flake8 isort - - run: | - flake8 . - black . --check - isort . + # - run: | + # flake8 . + # black . --check + # isort . test: needs: linting strategy: From 27ac10e41e344d90b3b7a2bd6085baf352c2c833 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:32:32 +0100 Subject: [PATCH 05/11] :) --- .github/workflows/tests.yml | 95 +++++++------------------------------ 1 file changed, 18 insertions(+), 77 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index cc0e48f..0ec6e9a 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,89 +1,30 @@ -name: test +name: Python package on: push jobs: - linting: - runs-on: ubuntu-latest - steps: - #---------------------------------------------- - # check-out repo and set-up python - #---------------------------------------------- - - uses: actions/checkout@v4 - - uses: actions/setup-python@v5 - #---------------------------------------------- - # load pip cache if cache exists - #---------------------------------------------- - - uses: actions/cache@v3 - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip - restore-keys: ${{ runner.os }}-pip - #---------------------------------------------- - # install and run linters - #---------------------------------------------- - - run: python -m pip install black flake8 isort - # - run: | - # flake8 . - # black . --check - # isort . - test: - needs: linting + build: + + runs-on: ${{ matrix.os }} strategy: - fail-fast: true matrix: - os: [ "ubuntu-latest", "macos-latest" ] - python-version: [ "3.9", "3.10", "3.11", "3.12" ] - django-version: [ "4", "5" ] - runs-on: ${{ matrix.os }} + os: [ubuntu-latest, macos-latest, windows-latest] + python-version: ["3.9", "3.10", "3.11", "3.12"] + steps: - #---------------------------------------------- - # check-out repo and set-up python - #---------------------------------------------- - - name: Check out repository - uses: actions/checkout@v4 - - name: Set up python ${{ matrix.python-version }} - id: setup-python - uses: actions/setup-python@v5 + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - #---------------------------------------------- - # ----- install & configure poetry ----- - #---------------------------------------------- - - name: Install Poetry - uses: snok/install-poetry@v1 - with: - virtualenvs-create: true - virtualenvs-in-project: true - #---------------------------------------------- - # load cached venv if cache exists - #---------------------------------------------- - - name: Load cached venv - id: cached-poetry-dependencies - uses: actions/cache@v3 - with: - path: .venv - key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} - #---------------------------------------------- - # install dependencies if cache does not exist - #---------------------------------------------- + - name: Install dependencies - if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' - run: poetry install --no-interaction --no-root - #---------------------------------------------- - # install your root project, if required - #---------------------------------------------- - - name: Install library - run: poetry install --no-interaction - #---------------------------------------------- - # add matrix specifics and run test suite - #---------------------------------------------- - - name: Install django ${{ matrix.django-version }} run: | - source .venv/bin/activate - pip install "Django==${{ matrix.django-version }}" - - name: Run tests + python -m pip install --upgrade pip + python -m pip install poetry + poetry install --with dev + + - name: Run tests with pytest run: | - source .venv/bin/activate - pytest tests/ - coverage report \ No newline at end of file + poetry run pytest \ No newline at end of file From 75b14ccd3bc2997d427b41d2d861a21a754d7cff Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 16:34:05 +0100 Subject: [PATCH 06/11] 3.11 --- .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 0ec6e9a..784e004 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -9,7 +9,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11"] steps: - uses: actions/checkout@v4 From fe48b9b114b82c6892c051de7c8b92355ebdcd45 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 17:17:12 +0100 Subject: [PATCH 07/11] added magellan test --- MTPHandler/core/abstractspecies.py | 155 ---- MTPHandler/core/blankstate.py | 106 --- MTPHandler/core/initcondition.py | 174 ---- poetry.lock | 1343 ++++++++++++++-------------- tests/magellan.xlsx | Bin 0 -> 14904 bytes tests/test_parsers.py | 26 + 6 files changed, 708 insertions(+), 1096 deletions(-) create mode 100644 tests/magellan.xlsx create mode 100644 tests/test_parsers.py diff --git a/MTPHandler/core/abstractspecies.py b/MTPHandler/core/abstractspecies.py index 64bd4d8..272669a 100644 --- a/MTPHandler/core/abstractspecies.py +++ b/MTPHandler/core/abstractspecies.py @@ -65,158 +65,3 @@ def get_vessel_id_reference(cls, value): raise TypeError( f"Expected types [Vessel, str] got '{type(value).__name__}' instead." ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) - - @validator("vessel_id") - def get_vessel_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - - from .vessel import Vessel - - if isinstance(value, Vessel): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [Vessel, str] got '{type(value).__name__}' instead." - ) diff --git a/MTPHandler/core/blankstate.py b/MTPHandler/core/blankstate.py index 510475a..2a112b1 100644 --- a/MTPHandler/core/blankstate.py +++ b/MTPHandler/core/blankstate.py @@ -43,109 +43,3 @@ def get_species_id_reference(cls, value): f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" " instead." ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) diff --git a/MTPHandler/core/initcondition.py b/MTPHandler/core/initcondition.py index 5eb3c2c..415c44f 100644 --- a/MTPHandler/core/initcondition.py +++ b/MTPHandler/core/initcondition.py @@ -46,177 +46,3 @@ def get_species_id_reference(cls, value): f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" " instead." ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - elif value is None: - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - elif value is None: - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_id_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - elif value is None: - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) - - @validator("species_id") - def get_species_reference(cls, value): - """Extracts the ID from a given object to create a reference""" - - from .abstractspecies import AbstractSpecies - - if isinstance(value, AbstractSpecies): - return value.id - elif isinstance(value, str): - return value - elif value is None: - return value - else: - raise TypeError( - f"Expected types [AbstractSpecies, str] got '{type(value).__name__}'" - " instead." - ) diff --git a/poetry.lock b/poetry.lock index 3c9bee5..66b6501 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "anytree" -version = "2.12.0" +version = "2.12.1" description = "Powerful and Lightweight Python Tree Data Structure with various plugins" optional = false python-versions = ">=3.7.2,<4" files = [ - {file = "anytree-2.12.0-py3-none-any.whl", hash = "sha256:b610433b95715625ea35e9009aa3e64261474c824fe9943dcbd618ed17cdeb58"}, - {file = "anytree-2.12.0.tar.gz", hash = "sha256:0dde0365cc8b1f3531e927694f39b903c360eadab2be09c50f3426ecca967949"}, + {file = "anytree-2.12.1-py3-none-any.whl", hash = "sha256:5ea9e61caf96db1e5b3d0a914378d2cd83c269dfce1fb8242ce96589fa3382f0"}, + {file = 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zMca?Fi2tsO2KM&ozF#pE=Tkd5icR%$~(!SyZi%J0_D zsU}6SKsosNkfoE#-76f}@agLEr(s2gDw)-iJmqB4Ejq^5!B#jXHp+J2?cTT2)53r@ z0&mlzTX%Kg?+hXs9_xI|VhN$uTvVt|D%NwtSB}IB7PVekEXh3gH$1{QJJO`_c0QWS zCF>Zz_WDX8q-Ef;pa;9O^Mh~tJxx`Ptm8rv-Ul=(&l$967H?Sl!iu=#u6+ucvO|~8 zYFEde)nr2sI(qZEC~THn8KTNU0{>e11Qm0&4`CQvMxeV2>@qkeq#5iq2vuB@;B)M? z#$@L0LC-bm!P>#Zzuc89k(uRbAdqg?L(jc;Y@&l={^F9zh4^nuP6Jj z`fnD>DMe&_N2LRlyM6XkbS z?{|RTCsBU^I@Yj^;chTRY%)dn2KK(=V_n7l{gx}+mzYsO)hp*#G$Ue*kD{%~b#Z literal 0 HcmV?d00001 diff --git a/tests/test_parsers.py b/tests/test_parsers.py new file mode 100644 index 0000000..2734465 --- /dev/null +++ b/tests/test_parsers.py @@ -0,0 +1,26 @@ +import pytest +from MTPHandler.core import Plate +from MTPHandler.readers.megellan_parser import read_magellan + + +def test_magellan(): + # Arrange + cls = Plate + path = "tests/magellan.xlsx" + ph = 7.0 + wavelength = 450.0 + + # Act + plate = read_magellan(cls, path, ph, wavelength) + + # Assert + assert isinstance(plate, Plate) + assert plate.n_rows == 8 + assert plate.n_columns == 12 + assert plate.measured_wavelengths == [450.0] + assert plate.temperature_unit == "C" + assert plate.temperatures == [37.1, 37.2, 37.1, 37.2, 36.9, 37.3, 37.2] + assert plate.time_unit == "s" + assert plate.times == [0, 900.0, 1802.0, 2700.0, 3600.0, 4502.0, 5400.0] + assert len(plate.wells) == 62 + assert plate.get_well("E8").get_measurement(450.0).absorptions[0] == 2.6871 From 6eb61eb45a8e14a4ff62d16b5f9f0dd9d3b84809 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 17:23:09 +0100 Subject: [PATCH 08/11] changed python dependency --- poetry.lock | 249 +++++++++++++++++++++++++++++++++++++++---------- pyproject.toml | 3 +- 2 files changed, 203 insertions(+), 49 deletions(-) diff --git a/poetry.lock b/poetry.lock index 66b6501..2a31251 100644 --- a/poetry.lock +++ b/poetry.lock @@ -109,6 +109,24 @@ files = [ docs = ["pytest"] test = ["hypothesis", "pytest", "pytest-remotedata"] +[[package]] +name = "asttokens" +version = "2.4.1" +description = "Annotate AST trees with source code positions" +optional = false +python-versions = "*" +files = [ + {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"}, + {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"}, +] + +[package.dependencies] +six = ">=1.12.0" + +[package.extras] +astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"] +test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"] + [[package]] name = "attrs" version = "23.2.0" @@ -473,6 +491,17 @@ files = [ docs = ["ipython", "matplotlib", "numpydoc", "sphinx"] tests = ["pytest", "pytest-cov", "pytest-xdist"] +[[package]] +name = "decorator" +version = "5.1.1" +description = "Decorators for Humans" +optional = false +python-versions = ">=3.5" +files = [ + {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"}, + {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"}, +] + [[package]] name = "dnspython" version = "2.5.0" @@ -544,6 +573,20 @@ files = [ [package.extras] test = ["pytest (>=6)"] +[[package]] +name = "executing" +version = "2.0.1" +description = "Get the currently executing AST node of a frame, and other information" +optional = false +python-versions = ">=3.5" +files = [ + {file = "executing-2.0.1-py2.py3-none-any.whl", hash = "sha256:eac49ca94516ccc753f9fb5ce82603156e590b27525a8bc32cce8ae302eb61bc"}, + {file = "executing-2.0.1.tar.gz", hash = "sha256:35afe2ce3affba8ee97f2d69927fa823b08b472b7b994e36a52a964b93d16147"}, +] + +[package.extras] +tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"] + [[package]] name = "fastjsonschema" version = "2.19.1" @@ -704,53 +747,71 @@ files = [ 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[[package]] name = "pathspec" version = "0.12.1" @@ -1604,6 +1689,20 @@ files = [ {file = "pathspec-0.12.1.tar.gz", hash = "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712"}, ] +[[package]] +name = "pexpect" +version = "4.9.0" +description = "Pexpect allows easy control of interactive console applications." +optional = false +python-versions = "*" +files = [ + {file = "pexpect-4.9.0-py2.py3-none-any.whl", hash = "sha256:7236d1e080e4936be2dc3e326cec0af72acf9212a7e1d060210e70a47e253523"}, + {file = "pexpect-4.9.0.tar.gz", hash = "sha256:ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f"}, +] + +[package.dependencies] +ptyprocess = ">=0.5" + [[package]] name = "pillow" version = "10.2.0" @@ -1734,6 +1833,45 @@ files = [ dev = ["pre-commit", "tox"] testing = ["pytest", "pytest-benchmark"] +[[package]] +name = "prompt-toolkit" +version = "3.0.43" +description = "Library for building powerful interactive command lines in Python" +optional = false +python-versions = ">=3.7.0" +files = [ + {file = "prompt_toolkit-3.0.43-py3-none-any.whl", hash = "sha256:a11a29cb3bf0a28a387fe5122cdb649816a957cd9261dcedf8c9f1fef33eacf6"}, + {file = "prompt_toolkit-3.0.43.tar.gz", hash = "sha256:3527b7af26106cbc65a040bcc84839a3566ec1b051bb0bfe953631e704b0ff7d"}, +] + +[package.dependencies] +wcwidth = "*" + +[[package]] +name = "ptyprocess" +version = "0.7.0" +description = "Run a subprocess in a pseudo terminal" +optional = false +python-versions = "*" +files = [ + {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"}, + {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"}, +] + +[[package]] +name = "pure-eval" +version = "0.2.2" +description = "Safely evaluate AST nodes without side effects" +optional = false +python-versions = "*" +files = [ + {file = "pure_eval-0.2.2-py3-none-any.whl", hash = "sha256:01eaab343580944bc56080ebe0a674b39ec44a945e6d09ba7db3cb8cec289350"}, + {file = "pure_eval-0.2.2.tar.gz", hash = "sha256:2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3"}, +] + +[package.extras] +tests = ["pytest"] + [[package]] name = "pydantic" version = "1.10.11" @@ -2417,6 +2555,25 @@ files = [ {file = "smmap-5.0.1.tar.gz", hash = "sha256:dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62"}, ] +[[package]] +name = "stack-data" +version = "0.6.3" +description = "Extract data from python stack frames and tracebacks for informative displays" +optional = false +python-versions = "*" +files = [ + {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"}, + {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"}, +] + +[package.dependencies] +asttokens = ">=2.1.0" +executing = ">=1.2.0" +pure-eval = "*" + +[package.extras] +tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"] + [[package]] name = "sympy" version = "1.12" @@ -2652,21 +2809,17 @@ files = [ watchmedo = ["PyYAML (>=3.10)"] [[package]] -name = "zipp" -version = "3.17.0" -description = "Backport of pathlib-compatible object wrapper for zip files" +name = "wcwidth" +version = "0.2.13" +description = "Measures the displayed width of unicode strings in a terminal" optional = false -python-versions = ">=3.8" +python-versions = "*" files = [ - {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, - {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, + {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, + {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, ] -[package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] - [metadata] lock-version = "2.0" -python-versions = ">=3.9,<3.13" -content-hash = "4d7f88bb8dfd9447b5b331edce631a678b45ed8f8abb8e29cfef4ee05e2af438" +python-versions = ">=3.10,<3.13" +content-hash = "81d4dcb2f4430c82107fca4631794332b2d0af9352d309f69263cea6dc3fb9e9" diff --git a/pyproject.toml b/pyproject.toml index 415206f..026a224 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,13 +12,14 @@ packages = [ ] [tool.poetry.dependencies] -python = ">=3.9,<3.13" +python = ">=3.10,<3.13" numpy = "1.24.4" sympy = "^1.12" sdrdm = {git = "https://github.com/JR-1991/software-driven-rdm.git", branch = "linking-refactor"} plotly = "^5.18.0" calipytion = {git = "https://github.com/FAIRChemistry/CaliPytion.git"} openpyxl = "^3.1.2" +ipython = "^8.21.0" [tool.poetry.group.dev.dependencies] mkdocs-material = "^9.5.7" From f1e5edfe738870fc08990806cd34084ba73fa29f Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 17:24:54 +0100 Subject: [PATCH 09/11] . --- .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 784e004..993b74e 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -9,7 +9,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v4 From 028e7896704ffa8516c4c5436c2b6eac6a90d032 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 17:28:54 +0100 Subject: [PATCH 10/11] comp with 3.10 and 3.11 --- .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 993b74e..ede29a7 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -9,7 +9,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest, windows-latest] - python-version: ["3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11"] steps: - uses: actions/checkout@v4 diff --git a/pyproject.toml b/pyproject.toml index 026a224..589b9f2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,7 +12,7 @@ packages = [ ] [tool.poetry.dependencies] -python = ">=3.10,<3.13" +python = ">=3.10,<3.12" numpy = "1.24.4" sympy = "^1.12" sdrdm = {git = "https://github.com/JR-1991/software-driven-rdm.git", branch = "linking-refactor"} From 536268eab27f0e4e1448f38ccad8af7b0cc01e85 Mon Sep 17 00:00:00 2001 From: haeussma <83341109+haeussma@users.noreply.github.com> Date: Tue, 6 Feb 2024 17:39:27 +0100 Subject: [PATCH 11/11] renamed --- .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 ede29a7..cfcce3c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -1,4 +1,4 @@ -name: Python package +name: Tests on: push