From f5b68a73e618935038a0a64eb30ff25e73adbe73 Mon Sep 17 00:00:00 2001 From: Peter Van Dyken Date: Thu, 14 Sep 2023 23:21:34 -0400 Subject: [PATCH] Overhaul of snakebids create Use copier instead of cookiecutter - Better feature set - Better documentation - More polished (e.g. typed codebase) Change starting workflow into a "welcome" workflow - Pregenerated empty data file based on the tutorial - workflow reads in the datafiles using generate_inputs and prints a welcome message Allow choice of build systems. App will be immediately installable and publishable End-to-end testing of app creation, dependency installation, and initial run --- .github/workflows/test.yml | 22 + containers/test-template/Dockerfile | 18 + containers/test-template/test-template.sh | 32 + poetry.lock | 727 +++++++++++------- pyproject.toml | 14 +- snakebids/admin.py | 28 +- snakebids/jinja2_ext/__init__.py | 0 snakebids/jinja2_ext/colorama.py | 11 + snakebids/jinja2_ext/vcs.py | 79 ++ snakebids/plugins/validator.py | 2 +- .../{{{ name_slug }} => }/README.md.jinja | 0 snakebids/project_template/copier.yaml | 87 ++- .../tests/data/dataset_description.json | 18 + snakebids/project_template/tests/data/sub-001 | 1 + ...'poetry' %}pyproject.toml{% endif %}.jinja | 48 ++ ...'poetry' %}pyproject.toml{% endif %}.jinja | 34 + ...setuptools' %}MANIFEST.in{% endif %}.jinja | 5 + .../.gitignore | 0 .../Makefile | 0 .../conf.py.jinja | 0 .../getting_started/installation.md.jinja | 0 .../index.md | 0 .../requirements.txt.jinja | 0 .../usage/app_cli.md.jinja | 0 .../usage/snakemake_cli.md | 0 .../{{ name_slug }}/setup.py.jinja | 46 -- .../{{name_slug}}/workflow/Snakefile | 53 -- .../{{name_slug}}/__init__.py | 0 .../{{name_slug}}/config/snakebids.yml | 21 +- .../pipeline_description.json.jinja | 0 .../{{name_slug}}/run.py.jinja | 2 +- .../{{name_slug}}/workflow/Snakefile | 39 + snakebids/tests/helpers.py | 20 +- snakebids/tests/test_template.py | 88 ++- 34 files changed, 957 insertions(+), 438 deletions(-) create mode 100644 containers/test-template/Dockerfile create mode 100755 containers/test-template/test-template.sh create mode 100644 snakebids/jinja2_ext/__init__.py create mode 100644 snakebids/jinja2_ext/colorama.py create mode 100644 snakebids/jinja2_ext/vcs.py rename snakebids/project_template/{{{ name_slug }} => }/README.md.jinja (100%) create mode 100644 snakebids/project_template/tests/data/dataset_description.json create mode 120000 snakebids/project_template/tests/data/sub-001 create mode 100644 snakebids/project_template/{% if build_system != 'poetry' %}pyproject.toml{% endif %}.jinja create mode 100644 snakebids/project_template/{% if build_system == 'poetry' %}pyproject.toml{% endif %}.jinja create mode 100644 snakebids/project_template/{% if build_system == 'setuptools' %}MANIFEST.in{% endif %}.jinja rename snakebids/project_template/{{{ name_slug }} => }/{% if create_doc_template %}docs{% endif %}/.gitignore (100%) rename snakebids/project_template/{{{ name_slug }} => }/{% if create_doc_template %}docs{% endif %}/Makefile (100%) rename snakebids/project_template/{{{ name_slug }} => }/{% if create_doc_template %}docs{% endif %}/conf.py.jinja (100%) rename snakebids/project_template/{{{ name_slug }} => }/{% if create_doc_template %}docs{% endif %}/getting_started/installation.md.jinja (100%) rename snakebids/project_template/{{{ name_slug }} => }/{% if create_doc_template %}docs{% endif %}/index.md (100%) rename snakebids/project_template/{{{ name_slug }} => }/{% if create_doc_template %}docs{% endif %}/requirements.txt.jinja (100%) rename snakebids/project_template/{{{ name_slug }} => }/{% if create_doc_template %}docs{% endif %}/usage/app_cli.md.jinja (100%) rename snakebids/project_template/{{{ name_slug }} => }/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md (100%) delete mode 100644 snakebids/project_template/{{ name_slug }}/setup.py.jinja delete mode 100644 snakebids/project_template/{{ name_slug }}/{{name_slug}}/workflow/Snakefile create mode 100644 snakebids/project_template/{{name_slug}}/__init__.py rename snakebids/project_template/{{{ name_slug }} => }/{{name_slug}}/config/snakebids.yml (92%) rename snakebids/project_template/{{{ name_slug }} => }/{{name_slug}}/pipeline_description.json.jinja (100%) rename snakebids/project_template/{{{ name_slug }} => }/{{name_slug}}/run.py.jinja (85%) create mode 100644 snakebids/project_template/{{name_slug}}/workflow/Snakefile diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 83fa32fb..401f97f2 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -58,6 +58,7 @@ jobs: - name: Install library run: poetry install --no-interaction --no-ansi + #---------------------------------------------- # run python style checks #---------------------------------------------- @@ -113,6 +114,27 @@ jobs: - name: Install dependencies if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' run: poetry install --no-interaction --no-root --no-ansi + + - name: Cache Template Testing Containers + uses: actions/cache@v3 + with: + path: container-test-template-cache + key: ${{ runner.os }}-go-build-cache-${{ hashFiles('containers/test-template/**') }} + + - name: Inject container-test-template-cache into docker + uses: reproducible-containers/buildkit-cache-dance@v2.1.2 + with: + cache-source: container-test-template-cache + - name: Build and push + uses: docker/build-push-action@v5 + with: + context: containers/test-template + cache-from: type=gha + cache-to: type=gha,mode=max + push: false + load: true + tags: snakebids/test-template + platforms: linux/amd64 #---------------------------------------------- # install your root project, if required #---------------------------------------------- diff --git a/containers/test-template/Dockerfile b/containers/test-template/Dockerfile new file mode 100644 index 00000000..5fd54422 --- /dev/null +++ b/containers/test-template/Dockerfile @@ -0,0 +1,18 @@ +FROM python:3.11.5 + +# Install and uninstall snakebids to cache it and it's dependences +RUN python -m pip install pipx && \ + pipx install poetry && \ + pipx install hatch && \ + pipx install pdm && \ + mkdir prebuild && \ + cd prebuild && \ + pip wheel snakebids && \ + cd .. && \ + rm -rf prebuild + +COPY ./test-template.sh /run/test-template.sh +ENV PATH="/root/.local/bin:$PATH" + +WORKDIR /work +ENTRYPOINT [ "/run/test-template.sh" ] diff --git a/containers/test-template/test-template.sh b/containers/test-template/test-template.sh new file mode 100755 index 00000000..14d44733 --- /dev/null +++ b/containers/test-template/test-template.sh @@ -0,0 +1,32 @@ +#!/bin/sh + +set -eu + +method="$1" +script_name="$2" + +cp -r /app/* /work +script="'${script_name}' tests/data tests/result participant -c1 --skip-bids-validation" +case "$method" in + "setuptools" ) + python -m venv .venv + .venv/bin/python -m pip install . + PATH=".venv/bin:$PATH" eval "$script" + ;; + "poetry" ) + poetry install + eval "poetry run $script" + ;; + "hatch" ) + hatch env create + eval "hatch env run -- $script" + ;; + "pdm" ) + pdm install + eval "pdm run $script" + ;; + * ) + >&2 echo "Invalid method" + exit 1 + ;; +esac diff --git a/poetry.lock b/poetry.lock index 63b0a374..80117950 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,19 @@ # This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +[[package]] +name = "annotated-types" +version = "0.5.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.7" +files = [ + {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"}, + {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"}, +] + +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} + [[package]] name = "appdirs" version = "1.4.4" @@ -182,13 +196,13 @@ files = [ [[package]] name = "cfgv" -version = "3.3.1" +version = "3.4.0" description = "Validate configuration and produce human readable error messages." optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.8" files = [ - {file = "cfgv-3.3.1-py2.py3-none-any.whl", hash = "sha256:c6a0883f3917a037485059700b9e75da2464e6c27051014ad85ba6aaa5884426"}, - {file = "cfgv-3.3.1.tar.gz", hash = "sha256:f5a830efb9ce7a445376bb66ec94c638a9787422f96264c98edc6bdeed8ab736"}, + {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, + {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, ] [[package]] @@ -288,13 +302,13 @@ files = [ [[package]] name = "click" -version = "8.1.6" +version = "8.1.7" description = "Composable command line interface toolkit" optional = false python-versions = ">=3.7" files = [ - {file = "click-8.1.6-py3-none-any.whl", hash = "sha256:fa244bb30b3b5ee2cae3da8f55c9e5e0c0e86093306301fb418eb9dc40fbded5"}, - {file = "click-8.1.6.tar.gz", hash = "sha256:48ee849951919527a045bfe3bf7baa8a959c423134e1a5b98c05c20ba75a1cbd"}, + {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, + {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, ] [package.dependencies] @@ -359,13 +373,13 @@ rich = "*" [[package]] name = "copier" -version = "8.1.0" +version = "8.3.0" description = "A library for rendering project templates." optional = false -python-versions = ">=3.7,<4.0" +python-versions = ">=3.8,<4.0" files = [ - {file = "copier-8.1.0-py3-none-any.whl", hash = "sha256:56537163b1b24441a63504ebf56b8db588dee20b48ef4fc374a6c5a2b43010c1"}, - {file = "copier-8.1.0.tar.gz", hash = "sha256:902b4eb65fafe7a1621991234d2ebf3bc3fc9323e64e3a2560a00c05c73f6229"}, + {file = "copier-8.3.0-py3-none-any.whl", hash = "sha256:a708e9b7c0eb7363ee5935f7a96a63a6f39b6da1d36f1c931d1ebd7711bb2ecf"}, + {file = "copier-8.3.0.tar.gz", hash = "sha256:051149721c811bfa84023fca5c23827917ac5f42ab6c2696dcb522b17aee7cae"}, ] [package.dependencies] @@ -378,11 +392,12 @@ jinja2-ansible-filters = ">=1.3.1" packaging = ">=23.0" pathspec = ">=0.9.0" plumbum = ">=1.6.9" -pydantic = ">=1.10.2,<2" +pydantic = ">=2.0.3" pygments = ">=2.7.1" pyyaml = ">=5.3.1" pyyaml-include = ">=1.2" questionary = ">=1.8.1" +typing-extensions = {version = ">=3.7.4,<5.0.0", markers = "python_version < \"3.9\""} [[package]] name = "datrie" @@ -440,6 +455,27 @@ files = [ {file = "distlib-0.3.7.tar.gz", hash = "sha256:9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8"}, ] +[[package]] +name = "docker" +version = "6.1.3" +description = "A Python library for the Docker Engine API." +optional = false +python-versions = ">=3.7" +files = [ + {file = "docker-6.1.3-py3-none-any.whl", hash = "sha256:aecd2277b8bf8e506e484f6ab7aec39abe0038e29fa4a6d3ba86c3fe01844ed9"}, + {file = "docker-6.1.3.tar.gz", hash = "sha256:aa6d17830045ba5ef0168d5eaa34d37beeb113948c413affe1d5991fc11f9a20"}, +] + +[package.dependencies] +packaging = ">=14.0" +pywin32 = {version = ">=304", markers = "sys_platform == \"win32\""} +requests = ">=2.26.0" +urllib3 = ">=1.26.0" +websocket-client = ">=0.32.0" + +[package.extras] +ssh = ["paramiko (>=2.4.3)"] + [[package]] name = "docopt" version = "0.6.2" @@ -488,13 +524,13 @@ packaging = ">=20.9" [[package]] name = "exceptiongroup" -version = "1.1.2" +version = "1.1.3" description = "Backport of PEP 654 (exception groups)" optional = false python-versions = ">=3.7" files = [ - {file = "exceptiongroup-1.1.2-py3-none-any.whl", hash = "sha256:e346e69d186172ca7cf029c8c1d16235aa0e04035e5750b4b95039e65204328f"}, - {file = "exceptiongroup-1.1.2.tar.gz", hash = "sha256:12c3e887d6485d16943a309616de20ae5582633e0a2eda17f4e10fd61c1e8af5"}, + {file = "exceptiongroup-1.1.3-py3-none-any.whl", hash = "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3"}, + {file = "exceptiongroup-1.1.3.tar.gz", hash = "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9"}, ] [package.extras] @@ -516,18 +552,21 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc [[package]] name = "filelock" -version = "3.12.2" +version = "3.12.3" description = "A platform independent file lock." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "filelock-3.12.2-py3-none-any.whl", hash = "sha256:cbb791cdea2a72f23da6ac5b5269ab0a0d161e9ef0100e653b69049a7706d1ec"}, - {file = "filelock-3.12.2.tar.gz", hash = "sha256:002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81"}, + {file = "filelock-3.12.3-py3-none-any.whl", hash = "sha256:f067e40ccc40f2b48395a80fcbd4728262fab54e232e090a4063ab804179efeb"}, + {file = "filelock-3.12.3.tar.gz", hash = "sha256:0ecc1dd2ec4672a10c8550a8182f1bd0c0a5088470ecd5a125e45f49472fac3d"}, ] +[package.dependencies] +typing-extensions = {version = ">=4.7.1", markers = "python_version < \"3.11\""} + [package.extras] -docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"] -testing = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "diff-cover (>=7.5)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"] +docs = ["furo (>=2023.7.26)", "sphinx (>=7.1.2)", "sphinx-autodoc-typehints (>=1.24)"] +testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)"] [[package]] name = "formulaic" @@ -581,13 +620,13 @@ smmap = ">=3.0.1,<6" [[package]] name = "gitpython" -version = "3.1.32" +version = "3.1.35" description = "GitPython is a Python library used to interact with Git repositories" optional = false python-versions = ">=3.7" files = [ - {file = "GitPython-3.1.32-py3-none-any.whl", hash = "sha256:e3d59b1c2c6ebb9dfa7a184daf3b6dd4914237e7488a1730a6d8f6f5d0b4187f"}, - {file = "GitPython-3.1.32.tar.gz", hash = "sha256:8d9b8cb1e80b9735e8717c9362079d3ce4c6e5ddeebedd0361b228c3a67a62f6"}, + {file = "GitPython-3.1.35-py3-none-any.whl", hash = "sha256:c19b4292d7a1d3c0f653858db273ff8a6614100d1eb1528b014ec97286193c09"}, + {file = "GitPython-3.1.35.tar.gz", hash = "sha256:9cbefbd1789a5fe9bcf621bb34d3f441f3a90c8461d377f84eda73e721d9b06b"}, ] [package.dependencies] @@ -693,12 +732,13 @@ pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_ve [[package]] name = "hypothesis" -version = "6.82.3" +version = "6.84.2" description = "A library for property-based testing" optional = false python-versions = ">=3.8" files = [ - {file = "hypothesis-6.82.3-py3-none-any.whl", hash = "sha256:7ff0f6a12d3cd9372e30f84d300e2468c3923e813198a93b9e479dda91858460"}, + {file = "hypothesis-6.84.2-py3-none-any.whl", hash = "sha256:b79209f2e0adf5a48d49467548a6c7e831ec100674e7aa611a444815d8d9e0dd"}, + {file = "hypothesis-6.84.2.tar.gz", hash = "sha256:82c7d4b696d211a8edd04dddd1077f13090b10263fee09648f7da389b749f7b0"}, ] [package.dependencies] @@ -724,13 +764,13 @@ zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2023.3)"] [[package]] name = "identify" -version = "2.5.26" +version = "2.5.27" description = "File identification library for Python" optional = false python-versions = ">=3.8" files = [ - {file = "identify-2.5.26-py2.py3-none-any.whl", hash = "sha256:c22a8ead0d4ca11f1edd6c9418c3220669b3b7533ada0a0ffa6cc0ef85cf9b54"}, - {file = "identify-2.5.26.tar.gz", hash = "sha256:7243800bce2f58404ed41b7c002e53d4d22bcf3ae1b7900c2d7aefd95394bf7f"}, + {file = "identify-2.5.27-py2.py3-none-any.whl", hash = "sha256:fdb527b2dfe24602809b2201e033c2a113d7bdf716db3ca8e3243f735dcecaba"}, + {file = "identify-2.5.27.tar.gz", hash = "sha256:287b75b04a0e22d727bc9a41f0d4f3c1bcada97490fa6eabb5b28f0e9097e733"}, ] [package.extras] @@ -876,17 +916,18 @@ testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-chec [[package]] name = "jaraco-functools" -version = "3.8.1" +version = "3.9.0" description = "Functools like those found in stdlib" optional = false python-versions = ">=3.8" files = [ - {file = "jaraco.functools-3.8.1-py3-none-any.whl", hash = "sha256:784718fbc5d70c5a7bd881c362d23d561913102eb1381cec21327c8ebda3351c"}, - {file = "jaraco.functools-3.8.1.tar.gz", hash = "sha256:e96a0d4ea455005a4092ce89a69ea0f7fb7e22807ad3b1008f9bf70c48d1cf2e"}, + {file = "jaraco.functools-3.9.0-py3-none-any.whl", hash = "sha256:df2e2b0aadd2dfcee2d7e0d7d083d5a5b68f4c8621e6915ae9819a90de65dd44"}, + {file = "jaraco.functools-3.9.0.tar.gz", hash = "sha256:8b137b0feacc17fef4bacee04c011c9e86f2341099c870a1d12d3be37b32a638"}, ] [package.dependencies] more-itertools = "*" +typing-extensions = {version = "*", markers = "python_version < \"3.11\""} [package.extras] docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] @@ -1007,6 +1048,21 @@ PyYAML = "*" [package.extras] test = ["pytest", "pytest-cov"] +[[package]] +name = "jinja2-time" +version = "0.2.0" +description = "Jinja2 Extension for Dates and Times" +optional = false +python-versions = "*" +files = [ + {file = 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(>=2.10)"] [[package]] @@ -2824,6 +2969,22 @@ files = [ {file = "wcwidth-0.2.6.tar.gz", hash = "sha256:a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0"}, ] +[[package]] +name = "websocket-client" +version = "1.6.3" +description = "WebSocket client for Python with low level API options" +optional = false +python-versions = ">=3.8" +files = [ + {file = "websocket-client-1.6.3.tar.gz", hash = "sha256:3aad25d31284266bcfcfd1fd8a743f63282305a364b8d0948a43bd606acc652f"}, + {file = "websocket_client-1.6.3-py3-none-any.whl", hash = "sha256:6cfc30d051ebabb73a5fa246efdcc14c8fbebbd0330f8984ac3bb6d9edd2ad03"}, +] + +[package.extras] +docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] +optional = ["python-socks", "wsaccel"] +test = ["websockets"] + [[package]] name = "wrapt" version = "1.15.0" @@ -2942,4 +3103,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.12" -content-hash = "1bd9e4a4c2c4abaa46d0e71932e5df31f905226f10a0f25f4cf9067416af730d" +content-hash = "9c7941c030d22b2eaff2967a8e7550a4dc40c3c2cf72e6b4a898f4711d940267" diff --git a/pyproject.toml b/pyproject.toml index 0ac00f85..fd52c569 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,7 +64,8 @@ scipy = [ { version = ">=1.10.0,<=1.10.1", python = "<3.9" }, { version = ">=1.10.0", python = ">=3.9" } ] -copier = "^8.1.0" +copier = ">=8.2.0" +jinja2-time = "^0.2.0" [tool.poetry.group.dev.dependencies] @@ -93,8 +94,8 @@ build-backend = "poetry_dynamic_versioning.backend" [tool.poe.tasks] setup = "pre-commit install" -quality = { shell = "isort snakebids && black snakebids && ruff snakebids && pyright" } -fix = { shell = "isort snakebids && black snakebids && ruff --fix snakebids"} +quality.shell = "isort snakebids && black snakebids && ruff snakebids && pyright" +fix.shell = "isort snakebids && black snakebids && ruff --fix snakebids" test = """ pytest --doctest-modules --ignore=docs \ --ignore=snakebids/project_template --benchmark-disable @@ -102,6 +103,13 @@ pytest --doctest-modules --ignore=docs \ mkinit = "mkinit --recursive --nomods --black -i snakebids" benchmark = "pytest --benchmark-only --benchmark-autosave" +[tool.poe.tasks.build-container] +args = [{ name = "container_id", positional = true, required = true }] +cmd = """ + docker build 'containers/${container_id}' \ + --tag 'snakebids/${container_id}:dev' +""" + [tool.isort] profile = "black" multi_line_output = 3 diff --git a/snakebids/admin.py b/snakebids/admin.py index 4b75f21f..18186214 100644 --- a/snakebids/admin.py +++ b/snakebids/admin.py @@ -1,10 +1,12 @@ """Script to generate a Snakebids project.""" import argparse +import sys from pathlib import Path +import copier # type: ignore import more_itertools as itx -from cookiecutter.main import cookiecutter # type: ignore +from colorama import Fore, Style import snakebids from snakebids.app import SnakeBidsApp @@ -12,10 +14,28 @@ def create_app(args: argparse.Namespace) -> None: - cookiecutter( - str(Path(itx.first(snakebids.__path__)) / "project_template"), - output_dir=args.output_dir, + output = Path(args.output_dir).resolve() + if not output.parent.exists(): + print( + f"{Fore.RED}{Style.BRIGHT}{output.parent}{Style.RESET_ALL}{Fore.RED} does " + f"not exist{Fore.RESET}", + file=sys.stderr, + ) + sys.exit(1) + print( + f"Creating Snakebids app at {Fore.GREEN}{output}{Fore.RESET}", file=sys.stderr ) + print(file=sys.stderr) + try: + copier.run_copy( # type: ignore + str(Path(itx.first(snakebids.__path__), "project_template")), + output, + data={"app_full_name": output.name}, + unsafe=True, + ) + except KeyboardInterrupt: + print(f"{Fore.RED}Aborted!{Fore.RESET}", file=sys.stderr) + sys.exit(1) def create_descriptor(args: argparse.Namespace) -> None: diff --git a/snakebids/jinja2_ext/__init__.py b/snakebids/jinja2_ext/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/snakebids/jinja2_ext/colorama.py b/snakebids/jinja2_ext/colorama.py new file mode 100644 index 00000000..927b40bf --- /dev/null +++ b/snakebids/jinja2_ext/colorama.py @@ -0,0 +1,11 @@ +from __future__ import annotations + +import jinja2.parser +from colorama import Fore +from jinja2.ext import Extension + + +class ColoramaExtension(Extension): + def __init__(self, env: jinja2.Environment): + super().__init__(env) + env.globals["Fore"] = Fore # type: ignore diff --git a/snakebids/jinja2_ext/vcs.py b/snakebids/jinja2_ext/vcs.py new file mode 100644 index 00000000..b7478ca6 --- /dev/null +++ b/snakebids/jinja2_ext/vcs.py @@ -0,0 +1,79 @@ +from __future__ import annotations + +import re +import subprocess +import sys +from pathlib import Path + +import jinja2.parser +from jinja2 import nodes +from jinja2.ext import Extension + + +class GitConfigExtension(Extension): + tags = {"gitconfig"} # noqa: RUF012 + _config: dict[str, str] + + def __init__(self, env: jinja2.Environment) -> None: + self._config = {} + + try: + config_list = subprocess.check_output( + [executable(), "config", "-l"], stderr=subprocess.STDOUT + ).decode() + + m = re.findall("(?ms)^([^=]+)=(.*?)$", config_list) + if m: + for group in m: + self._config[group[0]] = group[1] + except (subprocess.CalledProcessError, OSError): + pass + + def get(self, key: str, default: str | None = None) -> str | None: + return self._config.get(key, default) + + def __getitem__(self, item: str) -> str: + return self._config[item] + + def parse(self, parser: jinja2.parser.Parser): + lineno = next(parser.stream).lineno + + node = parser.parse_expression() + + if not isinstance(node, nodes.Const): + raise ValueError("Argument to `gitconfig` must be a string") + call_method = self.call_method( + "get", + [node], + lineno=lineno, + ) + return nodes.Output([call_method], lineno=lineno) + + +def executable() -> str: + _executable = None + + if sys.platform == "win32": + # Finding git via where.exe + where = "%WINDIR%\\System32\\where.exe" + paths = subprocess.check_output( + [where, "git"], shell=True, encoding="oem" + ).split("\n") + for path in paths: + if not path: + continue + + _path = Path(path.strip()) + try: + _path.relative_to(Path.cwd()) + except ValueError: + _executable = str(_path) + + break + else: + _executable = "git" + + if _executable is None: # type: ignore + raise RuntimeError("Unable to find a valid git executable") + + return _executable diff --git a/snakebids/plugins/validator.py b/snakebids/plugins/validator.py index b21fb2d5..7dbe311e 100644 --- a/snakebids/plugins/validator.py +++ b/snakebids/plugins/validator.py @@ -56,7 +56,7 @@ def __call__(self, app: SnakeBidsApp) -> None: temp.flush() try: subprocess.check_call( - ["bids-validator", app.config["bids_dirs"], "-c", temp.name] + ["bids-validator", app.config["bids_dir"], "-c", temp.name] ) # If successfully bids-validation performed diff --git a/snakebids/project_template/{{ name_slug }}/README.md.jinja b/snakebids/project_template/README.md.jinja similarity index 100% rename from snakebids/project_template/{{ name_slug }}/README.md.jinja rename to snakebids/project_template/README.md.jinja diff --git a/snakebids/project_template/copier.yaml b/snakebids/project_template/copier.yaml index 9d314da2..4df5e52f 100644 --- a/snakebids/project_template/copier.yaml +++ b/snakebids/project_template/copier.yaml @@ -1,11 +1,12 @@ full_name: type: str help: What is your name? - placeholder: " optional" + default: '{% gitconfig "user.name" %}' email: type: str help: What is your email? + default: '{% gitconfig "user.email" %}' github: type: str @@ -14,7 +15,6 @@ github: app_full_name: type: str help: What is the name of your app? - default: "{{ dst_path }}" validator: '{% if not app_full_name %}Required{% endif %}' app_description: @@ -24,6 +24,25 @@ app_description: app_version: default: "0.1.0" help: Starting version number for your app + validator: '{% if not app_version %}Required{% endif %}' + +build_system: + help: > + What build system would you like to use? If you don't know what this means, + choose setuptools + choices: + - setuptools + - poetry + - hatch + - flit + +# Flit and setuptools requires specifying license via Trove classifiers; too +# complicated to get via interactive prompt +license: + default: >- + {% if build_system != "flit" and build_system != "setuptools" %}MIT{% endif %} + help: Usage license for your app + when: "{{ build_system != 'flit' and build_system != 'setuptools' }}" create_doc_template: type: bool @@ -34,12 +53,74 @@ bids_version: when: false snakebids_version: - default: "0.0.0" + default: "0.9.2" + when: false + +snakemake_version: + default: "7.20" when: false name_slug: default: "{{ app_full_name|lower|replace(' ', '_')|replace('-', '_') }}" when: false +test_run_cmd: + default: "{{ name_slug }} tests/data tests/result participant -c1" + when: false + +_message_after_copy: > + Snakebids project successfully created in + {{ Fore.GREEN }}{{ _copier_conf.dst_path }}{{ Fore.RESET }} + + + Just a few steps before coding: + + + {{ Fore.BLUE }}1.{{ Fore.RESET }} Change into the project directory: + + $ cd {{ _copier_conf.dst_path }} + + {% if build_system == "poetry" -%} + {{ Fore.BLUE }}2.{{ Fore.RESET }} Install dependencies. + + $ poetry install + + {%- else -%} + {{ Fore.BLUE + "2." + Fore.RESET + """ Install dependencies. This may vary + depending on your tooling. The following are examples (the first example + should work on any python environment; the others require 3rd party tools): + """ | wordwrap(80)}} + + * {{Fore.YELLOW}}Virtual Environment and setuptools:{{Fore.RESET}} + $ python -m venv .venv + $ source .venv/bin/activate + $ pip install . + + * {{Fore.YELLOW}}Hatch:{{Fore.RESET}} + $ hatch env create + + * {{Fore.YELLOW}}PDM:{{Fore.RESET}} + $ pdm install + {%- endif %} + + + {{ Fore.BLUE }}3.{{Fore.RESET }} Perform a test run. + + {% if build_system == "poetry" %} + $ poetry run {{ test_run_cmd }} + + {%- else %} + * {{Fore.YELLOW}}Virtual Environment and setuptools:{{Fore.RESET}} + $ {{ test_run_cmd }} + + * {{Fore.YELLOW}}Hatch:{{Fore.RESET}} + $ hatch env run -- {{ test_run_cmd }} + + * {{Fore.YELLOW}}PDM:{{Fore.RESET}} + $ pdm run {{ test_run_cmd }} + {%- endif %} + _jinja_extensions: - jinja2_time.TimeExtension + - snakebids.jinja2_ext.vcs.GitConfigExtension + - snakebids.jinja2_ext.colorama.ColoramaExtension diff --git a/snakebids/project_template/tests/data/dataset_description.json b/snakebids/project_template/tests/data/dataset_description.json new file mode 100644 index 00000000..cec4e821 --- /dev/null +++ b/snakebids/project_template/tests/data/dataset_description.json @@ -0,0 +1,18 @@ +{ + "Acknowledgements": "Snakebids Development Team", + "Authors": [ + "Peter Van Dyken", + "Ali Khan", + "Tristan Kuehn", + "Jason Kai" + ], + "DatasetType": "raw", + "BIDSVersion": "1.4.1", + "HowToAcknowledge": "https://zenodo.org/record/8274278", + "License": "PDLL", + "Name": "Snakebids Test T1w Dataset (empty files)", + "ReferencesAndLinks": [ + "https://github.com/akhanf/snakebids", + "List of papers or websites" + ] + } diff --git a/snakebids/project_template/tests/data/sub-001 b/snakebids/project_template/tests/data/sub-001 new file mode 120000 index 00000000..30ebd731 --- /dev/null +++ b/snakebids/project_template/tests/data/sub-001 @@ -0,0 +1 @@ +../../../../docs/tutorial/bids/sub-001 \ No newline at end of file diff --git a/snakebids/project_template/{% if build_system != 'poetry' %}pyproject.toml{% endif %}.jinja b/snakebids/project_template/{% if build_system != 'poetry' %}pyproject.toml{% endif %}.jinja new file mode 100644 index 00000000..a70448d8 --- /dev/null +++ b/snakebids/project_template/{% if build_system != 'poetry' %}pyproject.toml{% endif %}.jinja @@ -0,0 +1,48 @@ +[project] +name = "{{ app_full_name }}" +version = "{{ app_version }}" +description = "{{ app_description }}" +readme = "README.md" +{% if license -%} +license = "{{ license }}" +{%- endif %} +{% if full_name or email -%} +authors = [ + { {{ '' }} + {%- if full_name -%} + name = "{{ full_name }}" + {%- endif -%} + {%- if full_name and email -%} + ,{{ ' ' }} + {%- endif -%} + {%- if email -%} + email = "{{ email }}" + {%- endif -%} + {{ ' ' }}} +] +{%- endif %} +classifiers = [ + "Programming Language :: Python :: 3", + "Operating System :: OS Independent", +] + +requires-python = ">=3.8,<3.12" +dependencies = [ + "snakemake >= {{ snakemake_version }}", + "snakebids >= {{ snakebids_version }}", +] + +[project.scripts] +{{ name_slug }} = "{{ name_slug }}.run:main" + +[build-system] +{% if build_system == "flit" -%} +requires = ["flit_core >=3.2,<4"] +build-backend = "flit_core.buildapi" +{%- elif build_system == "hatch" -%} +requires = ["hatchling"] +build-backend = "hatchling.build" +{%- else -%} +requires = ["setuptools"] +build-backend = "setuptools.build_meta" +{%- endif %} diff --git a/snakebids/project_template/{% if build_system == 'poetry' %}pyproject.toml{% endif %}.jinja b/snakebids/project_template/{% if build_system == 'poetry' %}pyproject.toml{% endif %}.jinja new file mode 100644 index 00000000..4c4b11b7 --- /dev/null +++ b/snakebids/project_template/{% if build_system == 'poetry' %}pyproject.toml{% endif %}.jinja @@ -0,0 +1,34 @@ +[tool.poetry] +name = "{{ app_full_name }}" +version = "{{ app_version }}" +description = "{{ app_description }}" +readme = "README.md" +{% if license -%} +license = "{{ license }}" +{%- endif %} +{% if full_name -%} +authors = [ + {% if email -%} + "{{ full_name }} <{{email}}>" + {%- else -%} + "{{ full_name }}" + {%- endif %} +] +{%- endif %} +classifiers = [ + "Programming Language :: Python :: 3", + "Operating System :: OS Independent", +] + +[tool.poetry.dependencies] +python = ">=3.8,<3.12" +snakemake = ">={{ snakemake_version }}" +snakebids = ">={{ snakebids_version }}" + +[tool.poetry.scripts] +{{ name_slug }} = "{{ name_slug }}.run:main" + + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/snakebids/project_template/{% if build_system == 'setuptools' %}MANIFEST.in{% endif %}.jinja b/snakebids/project_template/{% if build_system == 'setuptools' %}MANIFEST.in{% endif %}.jinja new file mode 100644 index 00000000..cba9b38a --- /dev/null +++ b/snakebids/project_template/{% if build_system == 'setuptools' %}MANIFEST.in{% endif %}.jinja @@ -0,0 +1,5 @@ +include {{ name_slug }}/**/*.yaml +include {{ name_slug }}/**/*.yml +include {{ name_slug }}/**/*.json +include {{ name_slug }}/**/Snakefile +include {{ name_slug }}/**/*.smk diff --git a/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/.gitignore b/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/.gitignore similarity index 100% rename from snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/.gitignore rename to snakebids/project_template/{% if create_doc_template %}docs{% endif %}/.gitignore diff --git a/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/Makefile b/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/Makefile similarity index 100% rename from snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/Makefile rename to snakebids/project_template/{% if create_doc_template %}docs{% endif %}/Makefile diff --git a/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/conf.py.jinja b/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/conf.py.jinja similarity index 100% rename from snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/conf.py.jinja rename to snakebids/project_template/{% if create_doc_template %}docs{% endif %}/conf.py.jinja diff --git a/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/getting_started/installation.md.jinja b/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/getting_started/installation.md.jinja similarity index 100% rename from snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/getting_started/installation.md.jinja rename to snakebids/project_template/{% if create_doc_template %}docs{% endif %}/getting_started/installation.md.jinja diff --git a/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/index.md b/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/index.md similarity index 100% rename from snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/index.md rename to snakebids/project_template/{% if create_doc_template %}docs{% endif %}/index.md diff --git a/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/requirements.txt.jinja b/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/requirements.txt.jinja similarity index 100% rename from snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/requirements.txt.jinja rename to snakebids/project_template/{% if create_doc_template %}docs{% endif %}/requirements.txt.jinja diff --git a/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/app_cli.md.jinja b/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/app_cli.md.jinja similarity index 100% rename from snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/app_cli.md.jinja rename to snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/app_cli.md.jinja diff --git a/snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md b/snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md similarity index 100% rename from snakebids/project_template/{{ name_slug }}/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md rename to snakebids/project_template/{% if create_doc_template %}docs{% endif %}/usage/snakemake_cli.md diff --git a/snakebids/project_template/{{ name_slug }}/setup.py.jinja b/snakebids/project_template/{{ name_slug }}/setup.py.jinja deleted file mode 100644 index 13ef84b7..00000000 --- a/snakebids/project_template/{{ name_slug }}/setup.py.jinja +++ /dev/null @@ -1,46 +0,0 @@ -import json - -import setuptools - -with open("README.md", encoding="utf-8") as fh: - long_description = fh.read() - -with open("pipeline_description.json", encoding="utf-8") as fh: - pipeline = json.load(fh) -name = pipeline["GeneratedBy"][0]["Name"] -description = pipeline["Name"] -version = pipeline["GeneratedBy"][0]["Version"] -optional_vals = { - attr: pipeline["GeneratedBy"][0].get(key) - for attr, key in [ - ("url", "CodeURL"), - ("author", "Author"), - ("author_email", "AuthorEmail"), - ] - if key in pipeline -} - -setuptools.setup( - name=name, - version=version, - description=description, - long_description=long_description, - long_description_content_type="text/x-rst", - packages=setuptools.find_packages(), - include_package_data=True, - classifiers=[ - "Programming Language :: Python :: 3", - "Operating System :: OS Independent", - ], - entry_points={ - "console_scripts": [ - "{{name_slug}}={{name_slug}}.run:main" - ] - }, - install_requires=[ - "snakebids>={{snakebids_version}}", - "snakemake", - ], - python_requires=">=3.7", - **optional_vals, -) diff --git a/snakebids/project_template/{{ name_slug }}/{{name_slug}}/workflow/Snakefile b/snakebids/project_template/{{ name_slug }}/{{name_slug}}/workflow/Snakefile deleted file mode 100644 index b934da01..00000000 --- a/snakebids/project_template/{{ name_slug }}/{{name_slug}}/workflow/Snakefile +++ /dev/null @@ -1,53 +0,0 @@ -#---- begin snakebids boilerplate ---------------------------------------------- - -from snakebids import bids, generate_inputs, get_wildcard_constraints - -configfile: workflow.source_path('../config/snakebids.yml') - -# Get input wildcards -inputs = generate_inputs( - bids_dir=config["bids_dir"], - pybids_inputs=config["pybids_inputs"], - pybidsdb_dir=config.get("pybidsdb_dir"), - pybidsdb_reset=config.get("pybidsdb_reset"), - derivatives=config.get("derivatives", None), - participant_label=config.get("participant_label", None), - exclude_participant_label=config.get("exclude_participant_label", None), - validate=not config.get("plugins.validator.skip", False) -) - -#this adds constraints to the bids naming -wildcard_constraints: **get_wildcard_constraints(config['pybids_inputs']) - -#---- end snakebids boilerplate ------------------------------------------------ - - -rule smooth: - input: inputs['bold'].path - output: - bids( - root=config['root'], - datatype='func', - desc='smooth{fwhm}mm', - suffix='bold.nii.gz', - **inputs['bold'].wildcards - ) - container: config['singularity']['fsl'] - log: - bids( - root='logs', - suffix='smooth.log', - fwhm='{fwhm}', - **inputs['bold'].wildcards - ) - params: sigma = lambda wildcards: f'{float(wildcards.fwhm)/2.355:0.2f}' - shell: 'fslmaths {input} -s {params.sigma} {output}' - - -rule all: - input: - inputs['bold'].expand( - rules.smooth.output, - fwhm = config['smoothing_fwhm'], - ) - default_target: True diff --git a/snakebids/project_template/{{name_slug}}/__init__.py b/snakebids/project_template/{{name_slug}}/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/snakebids/project_template/{{ name_slug }}/{{name_slug}}/config/snakebids.yml b/snakebids/project_template/{{name_slug}}/config/snakebids.yml similarity index 92% rename from snakebids/project_template/{{ name_slug }}/{{name_slug}}/config/snakebids.yml rename to snakebids/project_template/{{name_slug}}/config/snakebids.yml index 9b36f37f..f2249d8f 100644 --- a/snakebids/project_template/{{ name_slug }}/{{name_slug}}/config/snakebids.yml +++ b/snakebids/project_template/{{name_slug}}/config/snakebids.yml @@ -22,16 +22,16 @@ targets_by_analysis_level: # https://bids-standard.github.io/pybids/generated/bids.layout.BIDSLayout.html#bids.layout.BIDSLayout.get pybids_inputs: + t1w: + filters: + suffix: T1w + wildcards: + - subject bold: filters: - suffix: 'bold' - extension: '.nii.gz' - datatype: 'func' + suffix: bold wildcards: - subject - - session - - acquisition - - task - run #configuration for the command-line parameters to make available @@ -54,7 +54,7 @@ parse_args: help: Level of the analysis that will be performed. choices: *analysis_levels - --participant_label: + --participant-label: help: The label(s) of the participant(s) that should be analyzed. The label corresponds to sub- from the BIDS spec (so it does not include "sub-"). If this parameter is not @@ -62,7 +62,7 @@ parse_args: participants can be specified with a space separated list. nargs: '+' - --exclude_participant_label: + --exclude-participant-label: help: The label(s) of the participant(s) that should be excluded. The label corresponds to sub- from the BIDS spec (so it does not include "sub-"). If this parameter is not @@ -78,7 +78,7 @@ parse_args: # custom command-line parameters can then be added, these will get added to the config and also accessible to plugins # below are examples for plugin and custom parameters (e.g. config['smoothing_fwhm']) - --skip_bids_validation: + --skip-bids-validation: help: 'Skip validation of BIDS dataset. BIDS validation is performed by default using the bids-validator plugin (if installed/enabled) or with the pybids validator implementation (if bids-validator is not installed/enabled).' @@ -86,9 +86,6 @@ parse_args: action: "store_true" default: False - --smoothing_fwhm: - nargs: '+' - required: True #--- workflow specific configuration -- below is just an example: diff --git a/snakebids/project_template/{{ name_slug }}/{{name_slug}}/pipeline_description.json.jinja b/snakebids/project_template/{{name_slug}}/pipeline_description.json.jinja similarity index 100% rename from snakebids/project_template/{{ name_slug }}/{{name_slug}}/pipeline_description.json.jinja rename to snakebids/project_template/{{name_slug}}/pipeline_description.json.jinja diff --git a/snakebids/project_template/{{ name_slug }}/{{name_slug}}/run.py.jinja b/snakebids/project_template/{{name_slug}}/run.py.jinja similarity index 85% rename from snakebids/project_template/{{ name_slug }}/{{name_slug}}/run.py.jinja rename to snakebids/project_template/{{name_slug}}/run.py.jinja index f9426d23..1b782c1f 100755 --- a/snakebids/project_template/{{ name_slug }}/{{name_slug}}/run.py.jinja +++ b/snakebids/project_template/{{name_slug}}/run.py.jinja @@ -13,7 +13,7 @@ def get_parser(): def main(): app = SnakeBidsApp( - Path(__file__).resolve().parent.parent, # to get repository root + Path(__file__).resolve().parent, # to get repository root plugins=[BidsValidator()], ) app.run_snakemake() diff --git a/snakebids/project_template/{{name_slug}}/workflow/Snakefile b/snakebids/project_template/{{name_slug}}/workflow/Snakefile new file mode 100644 index 00000000..079a2d39 --- /dev/null +++ b/snakebids/project_template/{{name_slug}}/workflow/Snakefile @@ -0,0 +1,39 @@ +from snakebids import bids, generate_inputs, get_wildcard_constraints + +configfile: 'config/snakebids.yml' + +# Get input wildcards +inputs = generate_inputs( + bids_dir=config["bids_dir"], + pybids_inputs=config["pybids_inputs"], + pybidsdb_dir=config.get("pybidsdb_dir"), + pybidsdb_reset=config.get("pybidsdb_reset"), + derivatives=config.get("derivatives", None), + participant_label=config.get("participant_label", None), + exclude_participant_label=config.get("exclude_participant_label", None), + validate=not config.get("plugins.validator.skip", False) +) + + +rule all: + input: + inputs['t1w'].expand(), + inputs['bold'].expand() + default_target: True + params: + inputs=lambda wcards, input: "- " + "\n- ".join(input) + shell: + """ + cat < _F: + if sp.run(["docker"]).returncode != 0: + return pytest.mark.skip(reason="docker is not available on this machine")( + func + ) + if sp.run(["docker", "image", "inspect", container]).returncode != 0: + return pytest.mark.skip(reason=f"{container} is not built on this machine")( + func + ) + return func + + return inner def entity_to_wildcard(entities: str | Iterable[str], /): diff --git a/snakebids/tests/test_template.py b/snakebids/tests/test_template.py index 1f709796..3f0d138a 100644 --- a/snakebids/tests/test_template.py +++ b/snakebids/tests/test_template.py @@ -1,42 +1,68 @@ -from os.path import join +from __future__ import annotations + +import subprocess as sp from pathlib import Path +import copier # type: ignore import more_itertools as itx import pytest -from cookiecutter.main import cookiecutter # type: ignore import snakebids -from snakebids.app import SnakeBidsApp -from snakebids.cli import SnakebidsArgs +from snakebids.tests.helpers import needs_docker -def test_template_dry_runs_successfully(tmp_path: Path): +@needs_docker("snakebids/test-template:dev") +@pytest.mark.parametrize( + ["build", "venv"], + [ + ("setuptools", "setuptools"), + ("poetry", "poetry"), + ("hatch", "hatch"), + ("flit", "pdm"), + ], +) +def test_template_dry_runs_successfully(tmp_path: Path, build: str, venv: str): app_name = "snakebids_app" - cookiecutter( - join(itx.first(snakebids.__path__), "project_template"), - no_input=True, - output_dir=str(tmp_path), + data: dict[str, str | bool] = { + "full_name": "", + "email": "", + "app_full_name": app_name, + "github": "", + "app_description": "", + "build_system": build, + "app_version": "0.1.0", + "create_doc_template": False, + "license": "", + } + # poetry we need an author + if build == "poetry": + data["full_name"] = "John Doe" + data["email"] = "example@email.com" + + copier.run_copy( # type: ignore + str(Path(itx.first(snakebids.__path__), "project_template")), + tmp_path / app_name, + data=data, + unsafe=True, ) - app = SnakeBidsApp( - tmp_path / app_name / app_name, - args=SnakebidsArgs( - force=False, - outputdir=tmp_path / "out", - snakemake_args=["-n"], - args_dict={ - "bids_dir": Path("snakebids") / "tests" / "data" / "bids_bold", - "output_dir": tmp_path / "out", - "analysis_level": "participant", - "smoothing_fwhm": "1", - "filter_bold": None, - "wildcards_bold": None, - "path_bold": None, - "participant_label": None, - "exclude_participant_label": None, - "plugins.validator.skip": True, - }, - ), + cmd = sp.run( + [ + "docker", + "run", + "-v", + f"{tmp_path / app_name}:/app", + "--rm", + "snakebids/test-template:dev", + venv, + app_name, + ], + capture_output=True, + check=True, ) - with pytest.raises(SystemExit) as err: - app.run_snakemake() - assert err.value.code == 0 + # stdout: str = client.containers.run( + # "snakebids-test-template:dev", + # ["run/test-template.sh", "setuptools", app_name], + # volumes={str(tmp_path / app_name): { "bind": "/app", "mode": "rw"}}, + # auto_remove=True, + # ).decode() + assert "All set" in cmd.stdout.decode()