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+[package.extras] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] + +[metadata] +lock-version = "2.0" +python-versions = ">=3.9,<4" +content-hash = "e4a5f251ae6238d2c695caa04808e4fd0b7cd736738566e61779c3555eb96318" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..56c2da7 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,54 @@ +[tool.poetry] +name = "wps-tools" +version = "2.0.0" +description = "A collection of modules used to help create wps processes" +authors = [ + "Nikola Rados", + "Sangwon Lim", + "Cairo Sanders", + "Eric Yvorchuk ", +] +readme = "README.md" +homepage = "http://www.pacificclimate.org/" +repository = "https://github.com/pacificclimate/wps-tools" +classifiers=[ + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", +] +packages = [ + {include = "wps_tools"}, +] +include = [ + "tests/data/*.nc", + "tests/processes/*.py", +] + +[[tool.poetry.source]] +name = "pcic" +url = "https://pypi.pacificclimate.org/simple" +priority = "supplemental" + +[tool.poetry.dependencies] +python = ">=3.9,<4" +pywps = ">=4.2.6" +nchelpers = { version = "^5.5.11", source = "pcic" } +netCDF4 = ">=1.5.4" +beautifulsoup4 = "==4.9.3" +rpy2 = "==3.3.6" + + +[tool.poetry.group.dev.dependencies] +pytest = "^8.2.1" +black = "^22.3.0" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + +[tool.pytest.ini_options] +markers = [ + "online: marks tests that use online resources (deselect with '-m \"not online\"')", + "slow: marks tests that are slow (deselect with '-m \"not slow\"')", +] From 334cd0390f14daa3391f0024c06ac8dfbb3aa280 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 11:02:41 -0700 Subject: [PATCH 02/10] Update README.md --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 46aac65..525ce69 100644 --- a/README.md +++ b/README.md @@ -25,15 +25,15 @@ These functions gather PyWPS inputs, build PyWPS outputs, and handle logging inf ## Installation as GitHub Repository -Clone the repo onto the target machine. Python installation should be done using the `pipenv` tool. The required dependencies can be installed using +Clone the repo onto the target machine. Python installation should be done using the `poetry` tool. The required dependencies can be installed using ```bash -pipenv install +poetry install ``` This also creates a virtual environment that can be activated using ```bash -pipenv shell +poetry shell ``` ## Installation and Usage as Package @@ -59,7 +59,7 @@ Once the repository is cloned and the required development packages are installe More Python packages are required to run the tests and they can be installed by executing ```bash -pipenv install --dev +poetry install --group dev ``` The entire test suite can then be run by executing @@ -78,14 +78,14 @@ pytest tests/test_utils.py::test_is_opendap_url To create a versioned release: -1. Increment `__version__` in `setup` +1. Increment `version` in `pyproject.toml` 2. Summarize the changes from the last release in `NEWS.md` 3. Commit these changes, then tag the release: ```bash -git add setup NEWS.md +git add pyproject.toml NEWS.md git commit -m"Bump to version x.x.x" git tag -a -m"x.x.x" x.x.x git push --follow-tags ``` -4. [Github Actions](https://github.com/pacificclimate/wps-tools/blob/i16-update-documentation/.github/workflows/pypi-publish.yml) will automatically build and publish the package to our pypi server +4. [Github Actions](https://github.com/pacificclimate/wps-tools/blob/master/.github/workflows/pypi-publish.yml) will automatically build and publish the package to our pypi server From f3016213a0262602732b12c24bdd4f2e26b0f593 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 11:02:51 -0700 Subject: [PATCH 03/10] Update CI actions --- .github/workflows/pypi-publish.yml | 19 +++++++++--------- .github/workflows/python-ci.yml | 31 ++++++++++++++---------------- 2 files changed, 24 insertions(+), 26 deletions(-) diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml index defab4b..899c951 100644 --- a/.github/workflows/pypi-publish.yml +++ b/.github/workflows/pypi-publish.yml @@ -8,22 +8,23 @@ on: jobs: publish: - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 steps: - uses: actions/checkout@v2 - name: Set up Python uses: actions/setup-python@v2 with: - python-version: '3.8' - - name: Install dependencies + python-version: '3.10' + - name: Install Poetry run: | - pip install -U pip - pip install Sphinx==2.4.4 setuptools wheel twine + curl -sSL https://install.python-poetry.org | python3 - - name: Build and publish env: - TWINE_USERNAME: ${{ secrets.pcic_at_pypi_username }} - TWINE_PASSWORD: ${{ secrets.pcic_at_pypi_password }} + PCIC_PYPI_USERNAME: ${{ secrets.pcic_at_pypi_username }} + PCIC_PYPI_PASSWORD: ${{ secrets.pcic_at_pypi_password }} run: | - python setup.py sdist bdist_wheel - twine upload --repository-url https://pypi.pacificclimate.org/ --skip-existing -u $TWINE_USERNAME -p $TWINE_PASSWORD dist/* + poetry config repositories.pcic https://pypi.pacificclimate.org/ + poetry config http-basic.pcic $PCIC_PYPI_USERNAME $PCIC_PYPI_PASSWORD + poetry build + poetry publish -r pcic diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index a085c2e..46f0051 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -8,7 +8,7 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python-version: [3.7, 3.8] + python-version: ["3.9, "3.10", "3.11"] steps: - uses: actions/checkout@v2 @@ -17,38 +17,35 @@ jobs: with: python-version: ${{ matrix.python-version }} - - name: Install cdo and pipenv + - name: Install cdo and poetry run: | sudo apt-get update sudo apt-get install cdo - pip install -U pip pipenv + curl -sSL https://install.python-poetry.org | python3 - + echo "$HOME/.local/bin" >> $GITHUB_PATH - - id: cache-pipenv + - id: cache-poetry uses: actions/cache@v2 with: - path: ~/.local/share/virtualenvs - key: ${{ runner.os }}-pipenv-${{ hashFiles('**/Pipfile.lock') }} + path: ~/.cache/pypoetry/virtualenvs + key: ${{ runner.os }}-poetry-${{ hashFiles('**/poetry.lock') }} - name: Install dependencies if changed - if: steps.cache-pipenv.outputs.cache-hit != 'true' && ${{ matrix.python-version == '3.8' }} + if: ${{ steps.cache-poetry.outputs.cache-hit != 'true' }} run: | - pipenv install --deploy --dev - - - name: Re-install dependencies if alternative python version - if: ${{ matrix.python-version != '3.8' }} - run: | - mv Pipfile.lock do-not-use - pipenv install --python ${{ matrix.python-version }} --dev + poetry env use python${{ matrix.python-version }} + poetry install --group dev + poetry run pip install -e . - name: Test with pytest (full) if: github.ref == 'refs/heads/master' run: | - pipenv run py.test -m "not online" -v + poetry run py.test -m "not online" -v - name: Test with pytest (fast) if: github.ref != 'refs/heads/master' run: | - pipenv run py.test -m "not online and not slow" -v + poetry run py.test -m "not online and not slow" -v - name: Code Quality - run: pipenv run black . --check + run: poetry run black . --check From ff1cd60478b8f31e7cb66189e6689ea7057d4d6f Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 11:16:24 -0700 Subject: [PATCH 04/10] Fix python-ci.yml --- .github/workflows/python-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 46f0051..8011d31 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -8,7 +8,7 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python-version: ["3.9, "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11"] steps: - uses: actions/checkout@v2 From 79452d72c0e8ba6d69b7ab2facb3b1fbdc56f5c8 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 11:19:18 -0700 Subject: [PATCH 05/10] Fix python-ci.yml again --- .github/workflows/python-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 8011d31..e0ad12c 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -34,7 +34,7 @@ jobs: if: ${{ steps.cache-poetry.outputs.cache-hit != 'true' }} run: | poetry env use python${{ matrix.python-version }} - poetry install --group dev + poetry install --with=dev poetry run pip install -e . - name: Test with pytest (full) From 4c557ca94d91de69618a8d0b14f4e0ddf5c75327 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 11:20:05 -0700 Subject: [PATCH 06/10] Format with black --- tests/conftest.py | 5 ++++- tests/test_R.py | 19 +++++++++++++----- tests/test_file_handling.py | 19 ++++++++++++++---- tests/test_io.py | 5 ++++- tests/test_output_handling.py | 14 +++++++++++--- tests/test_testing.py | 24 ++++++++++++++++++++--- wps_tools/R.py | 36 +++++++++++++++++------------------ wps_tools/file_handling.py | 22 ++++++++++----------- 8 files changed, 98 insertions(+), 46 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 6c575ce..7ee8501 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -101,7 +101,10 @@ def __init__(self): } inputs = [ LiteralInput( - "string", "String", abstract="Enter string.", data_type="string", + "string", + "String", + abstract="Enter string.", + data_type="string", ) ] outputs = [ diff --git a/tests/test_R.py b/tests/test_R.py index 63a1296..320966e 100644 --- a/tests/test_R.py +++ b/tests/test_R.py @@ -14,7 +14,8 @@ @pytest.mark.parametrize( - ("package"), [("base"), ("utils")], + ("package"), + [("base"), ("utils")], ) def test_get_package(package): pkg = get_package(package) @@ -41,7 +42,9 @@ def test_load_rdata_to_python(r_file, r_object_name): @pytest.mark.parametrize( ("file_", "obj_name"), - [(resource_filename("tests", "data/expected_days_data.rda"), "autumn_days"),], + [ + (resource_filename("tests", "data/expected_days_data.rda"), "autumn_days"), + ], ) def test_load_rdata_to_python_err(file_, obj_name): with pytest.raises(ProcessError) as e: @@ -53,7 +56,11 @@ def test_load_rdata_to_python_err(file_, obj_name): @pytest.mark.parametrize( - ("r_name", "py_var"), [("str_ex", "string"), ("int_ex", 300),], + ("r_name", "py_var"), + [ + ("str_ex", "string"), + ("int_ex", 300), + ], ) def test_save_python_to_rdata(r_name, py_var): with NamedTemporaryFile( @@ -68,14 +75,16 @@ def test_save_python_to_rdata(r_name, py_var): @pytest.mark.parametrize( - ("name"), [("hello.world"), ("r_name")], + ("name"), + [("hello.world"), ("r_name")], ) def test_r_valid_name(name): r_valid_name(name) @pytest.mark.parametrize( - ("name"), [(".2"), ("if"), ("two words")], + ("name"), + [(".2"), ("if"), ("two words")], ) def test_r_valid_name_err(name): with pytest.raises(ProcessError) as e: diff --git a/tests/test_file_handling.py b/tests/test_file_handling.py index 9577009..4dcb6c2 100644 --- a/tests/test_file_handling.py +++ b/tests/test_file_handling.py @@ -26,7 +26,11 @@ @pytest.mark.online @pytest.mark.parametrize( - ("url"), [url_path(nc_file, "opendap"), local_path(nc_file),], + ("url"), + [ + url_path(nc_file, "opendap"), + local_path(nc_file), + ], ) def test_is_opendap_url(url): if "docker" in url: @@ -38,7 +42,8 @@ def test_is_opendap_url(url): @pytest.mark.parametrize( - ("nc_input"), [[NCInput(file=local_path(nc_file))]], + ("nc_input"), + [[NCInput(file=local_path(nc_file))]], ) def test_get_filepaths_local(nc_input): paths = get_filepaths(nc_input) @@ -52,7 +57,10 @@ def test_get_filepaths_local(nc_input): ("nc_input"), [ [NCInput(url=url_path(nc_file, "opendap"))], - [NCInput(file=local_path(nc_file)), NCInput(url=url_path(nc_file, "opendap")),], + [ + NCInput(file=local_path(nc_file)), + NCInput(url=url_path(nc_file, "opendap")), + ], ], ) def test_get_filepaths_online(nc_input): @@ -119,7 +127,10 @@ def test_copy_http_content(http, expected): @pytest.mark.online @pytest.mark.parametrize( ("url_type", "url"), - [("http", url_path(nc_file, "http")), ("opendap", url_path(nc_file, "opendap")),], + [ + ("http", url_path(nc_file, "http")), + ("opendap", url_path(nc_file, "opendap")), + ], ) def test_url_handler(url_type, url): processed = url_handler("/tmp", url) diff --git a/tests/test_io.py b/tests/test_io.py index a2a94f7..af1f73a 100644 --- a/tests/test_io.py +++ b/tests/test_io.py @@ -19,7 +19,10 @@ def run_args_collection(wps_test_process_multi_input, file, csv, argc): ("file", "argc"), [ ( - [local_path("tiny_daily_pr.nc"), local_path("tiny_daily_prsn.nc"),], + [ + local_path("tiny_daily_pr.nc"), + local_path("tiny_daily_prsn.nc"), + ], {"file": 2, "csv_input": 1, "argc": 1}, ) ], diff --git a/tests/test_output_handling.py b/tests/test_output_handling.py index f602750..3950498 100644 --- a/tests/test_output_handling.py +++ b/tests/test_output_handling.py @@ -27,7 +27,8 @@ def test_nc_to_dataset(url): @pytest.mark.parametrize( - ("url"), [local_path("gsl.json")], + ("url"), + [local_path("gsl.json")], ) def test_json_to_dict(url): output_dict = json_to_dict(url) @@ -85,7 +86,13 @@ def test_auto_construct_outputs_online(outputs, expected_types): @pytest.mark.parametrize( - ("outputs", "expected_types"), [(["test string"], [str, str],)], + ("outputs", "expected_types"), + [ + ( + ["test string"], + [str, str], + ) + ], ) def test_auto_construct_outputs_local(txt_file, outputs, expected_types): outputs.append(f"file://{txt_file.name}") @@ -94,7 +101,8 @@ def test_auto_construct_outputs_local(txt_file, outputs, expected_types): @pytest.mark.parametrize( - ("output"), ["https://test_metalinks.meta4"], + ("output"), + ["https://test_metalinks.meta4"], ) def test_get_metalink_content(mock_metalink, output): for file_ in get_metalink_content(output): diff --git a/tests/test_testing.py b/tests/test_testing.py index 43a2153..e3f01be 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -44,7 +44,13 @@ def test_run_wps_process(wps_test_process, string): @pytest.mark.parametrize( - "bird", [("thunderbird"), ("sandpiper"), ("osprey"), ("chickadee"),] + "bird", + [ + ("thunderbird"), + ("sandpiper"), + ("osprey"), + ("chickadee"), + ], ) @pytest.mark.parametrize("expected", ["http://localhost:5000/wps"]) def test_get_target_url_local(mock_local_url, bird, expected): @@ -52,7 +58,13 @@ def test_get_target_url_local(mock_local_url, bird, expected): @pytest.mark.parametrize( - "bird", [("thunderbird"), ("sandpiper"), ("osprey"), ("chickadee"),] + "bird", + [ + ("thunderbird"), + ("sandpiper"), + ("osprey"), + ("chickadee"), + ], ) @pytest.mark.parametrize("expected", ["http://docker-dev03.pcic.uvic.ca/somebird"]) def test_get_target_url_dev(mock_dev_url, bird, expected): @@ -60,7 +72,13 @@ def test_get_target_url_dev(mock_dev_url, bird, expected): @pytest.mark.parametrize( - "bird", [("thunderbird"), ("sandpiper"), ("osprey"), ("chickadee"),] + "bird", + [ + ("thunderbird"), + ("sandpiper"), + ("osprey"), + ("chickadee"), + ], ) def test_get_target_url(bird): assert bird in get_target_url(bird) diff --git a/wps_tools/R.py b/wps_tools/R.py index 9e25a37..980731a 100644 --- a/wps_tools/R.py +++ b/wps_tools/R.py @@ -10,14 +10,14 @@ def get_package(package): """ - Exposes all R objects in package as Python objects after - checking that it is installed. + Exposes all R objects in package as Python objects after + checking that it is installed. - Parameters: - package (str): the name of an R package + Parameters: + package (str): the name of an R package - Returns: - Exposed R package + Returns: + Exposed R package """ if isinstalled(package): return importr(package) @@ -27,15 +27,15 @@ def get_package(package): def load_rdata_to_python(r_file, r_object_name): """ - Loads R objects from a .rda or .Rdata file into the embedded R - environment, then exposes that object as a Python object. + Loads R objects from a .rda or .Rdata file into the embedded R + environment, then exposes that object as a Python object. - Parameters: - r_file (str): path to an .rda or .rdata file - r_object_name (str): name of an R object from the r_file + Parameters: + r_file (str): path to an .rda or .rdata file + r_object_name (str): name of an R object from the r_file - Returns: - Exposed R object as a python object + Returns: + Exposed R object as a python object """ try: robjects.r(f"load(file='{r_file}')") @@ -55,12 +55,12 @@ def load_rdata_to_python(r_file, r_object_name): def save_python_to_rdata(r_name, py_var, r_file): """ - Saves a Python object as an R object to a Rdata (.rda) file + Saves a Python object as an R object to a Rdata (.rda) file - Parameters: - r_name (str): name to give the oject in the R environment - py_var (any type): python variable to save to the R environment - r_file (str): path to rdata file + Parameters: + r_name (str): name to give the oject in the R environment + py_var (any type): python variable to save to the R environment + r_file (str): path to rdata file """ robjects.r.assign(r_name, py_var) robjects.r(f"save({r_name}, file='{r_file}')") diff --git a/wps_tools/file_handling.py b/wps_tools/file_handling.py index 74261bd..f394c21 100644 --- a/wps_tools/file_handling.py +++ b/wps_tools/file_handling.py @@ -76,7 +76,7 @@ def get_filepaths(nc_input): Each path in nc_input is checked to determine if it is an OpenDAP url. If so, then the url is appended to the path list. If not, then whether or not it's a valid - netcdf file is checked. If so, then the path is appended to the list. If not, then + netcdf file is checked. If so, then the path is appended to the list. If not, then a ProcessError is raised due to an invalid input. Parameters: @@ -162,16 +162,16 @@ def build_meta_link( def copy_http_content(http, file): """ - This function is implemented to copy the content of a file passed - as an http address to a local file. - - Parameters: - http (str): http address containing the desired content - file (file object): path to the - file that the content will be copied to - Returns: - Path to the copied file in /tmp directory - """ + This function is implemented to copy the content of a file passed + as an http address to a local file. + + Parameters: + http (str): http address containing the desired content + file (file object): path to the + file that the content will be copied to + Returns: + Path to the copied file in /tmp directory + """ file.write(get(http).content) return file.name From 58073d57e0ddcb2cf4564263f1be1a29ffc9cd5f Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 11:32:13 -0700 Subject: [PATCH 07/10] Specify extras from setup.py --- poetry.lock | 17 +++++++++++------ pyproject.toml | 7 ++++++- 2 files changed, 17 insertions(+), 7 deletions(-) diff --git a/poetry.lock b/poetry.lock index 28fb6f2..a7bfceb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -109,7 +109,7 @@ files = [ name = "cffi" version = "1.16.0" description = "Foreign Function Interface for Python calling C code." -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "cffi-1.16.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6b3d6606d369fc1da4fd8c357d026317fbb9c9b75d36dc16e90e84c26854b088"}, @@ -1097,7 +1097,7 @@ testing = ["pytest", "pytest-benchmark"] name = "pycparser" version = "2.22" description = "C parser in Python" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "pycparser-2.22-py3-none-any.whl", hash = "sha256:c3702b6d3dd8c7abc1afa565d7e63d53a1d0bd86cdc24edd75470f4de499cfcc"}, @@ -1425,7 +1425,7 @@ files = [ name = "rpy2" version = "3.3.6" description = "Python interface to the R language (embedded R)" -optional = false +optional = true python-versions = "*" files = [ {file = "rpy2-3.3.6.tar.gz", hash = "sha256:ce063f3286e717b3914728ad23ec7db0a0f117ba3ade5ada8a250700779f6e77"}, @@ -1590,7 +1590,7 @@ files = [ name = "tzdata" version = "2024.1" description = "Provider of IANA time zone data" -optional = false +optional = true python-versions = ">=2" files = [ {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"}, @@ -1601,7 +1601,7 @@ files = [ name = "tzlocal" version = "5.2" description = "tzinfo object for the local timezone" -optional = false +optional = true python-versions = ">=3.8" files = [ {file = "tzlocal-5.2-py3-none-any.whl", hash = "sha256:49816ef2fe65ea8ac19d19aa7a1ae0551c834303d5014c6d5a62e4cbda8047b8"}, @@ -1683,7 +1683,12 @@ files = [ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +[extras] +complete = ["rpy2"] +r = ["rpy2"] +test = [] + [metadata] lock-version = "2.0" python-versions = ">=3.9,<4" -content-hash = "e4a5f251ae6238d2c695caa04808e4fd0b7cd736738566e61779c3555eb96318" +content-hash = "8ff93909979347958cc66232db69bda018a3d3b61025e7c47010a5329d1f0db0" diff --git a/pyproject.toml b/pyproject.toml index 56c2da7..9485d79 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,13 +36,18 @@ pywps = ">=4.2.6" nchelpers = { version = "^5.5.11", source = "pcic" } netCDF4 = ">=1.5.4" beautifulsoup4 = "==4.9.3" -rpy2 = "==3.3.6" +rpy2 = {version = "==3.3.6", optional = true } [tool.poetry.group.dev.dependencies] pytest = "^8.2.1" black = "^22.3.0" +[tool.poetry.extras] +r = ["rpy2"] +test = ["pytest", "black"] +complete = ["rpy2", "pytest", "black"] + [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" From 9877ca32a235dd3204c65650dceb624c1f6aefdc Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 11:33:40 -0700 Subject: [PATCH 08/10] Remove previous installation files --- Pipfile | 23 -- Pipfile.lock | 856 --------------------------------------------------- pytest.ini | 5 - 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- -__version__ = (2, 0, 0) - - -# Detail different installation scenarios -extras_require = { - "r": ["rpy2 == 3.3.6"], -} -extras_require["complete"] = { - requirements for scenario in extras_require.values() for requirements in scenario -} -extras_require["test"] = ["pytest == 5.4.3", "black == 19.10b0"] - -# Main installation requirements -install_requires = [ - "pywps >= 4.2.6", - "nchelpers == 5.5.7", - "netCDF4 >= 1.5.4", - "beautifulsoup4 == 4.9.3", -] - -setup( - name="wps_tools", - description="A collection of modules used to help create wps processes", - keywords="wps pywps wps_tools", - version=".".join(str(d) for d in __version__), - url="https://github.com/pacificclimate/wps-tools", - author="Eric Yvorchuk", - author_email="eyvorchuk@uvic.ca", - packages=["wps_tools"], - package_data={ - "wps-tools": ["tests/data/*.nc", "tests/processes/*.py"], - "tests": ["tests/data/*", "processes/*.py"], - }, - include_package_data=True, - install_requires=install_requires, - extras_require=extras_require, - classifiers=[ - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - ], -) From 6c0f3c51219e6a7183dfd44a827ec0e95787a77c Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 11:36:05 -0700 Subject: [PATCH 09/10] Install extra dependencies in CI --- .github/workflows/python-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index e0ad12c..4b72f29 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -34,7 +34,7 @@ jobs: if: ${{ steps.cache-poetry.outputs.cache-hit != 'true' }} run: | poetry env use python${{ matrix.python-version }} - poetry install --with=dev + poetry install --extras "complete" poetry run pip install -e . - name: Test with pytest (full) From 0a3a99d29dd3ce118b671d424c9364fc58fc6597 Mon Sep 17 00:00:00 2001 From: Eric Yvorchuk Date: Fri, 24 May 2024 11:44:08 -0700 Subject: [PATCH 10/10] Update README.md --- README.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 525ce69..771eb72 100644 --- a/README.md +++ b/README.md @@ -31,6 +31,11 @@ Clone the repo onto the target machine. Python installation should be done using poetry install ``` +The additional R dependencies can be installed using +```bash +poetry install --extras "r" +``` + This also creates a virtual environment that can be activated using ```bash poetry shell @@ -59,7 +64,7 @@ Once the repository is cloned and the required development packages are installe More Python packages are required to run the tests and they can be installed by executing ```bash -poetry install --group dev +poetry install --extras "complete" ``` The entire test suite can then be run by executing