From a830458b30d683590ee35e69b984efba21bf5e3f Mon Sep 17 00:00:00 2001 From: quanpython Date: Fri, 3 Nov 2023 10:08:57 +0700 Subject: [PATCH 1/5] replace setuptools to poetry --- docker-compose.dev.yml | 2 +- docker-compose.test.yml | 6 +- docker-compose.yml | 2 +- .../each_platforms_for_developer.md | 4 +- .../each_platforms_for_developer_use_mamba.md | 4 +- poetry.lock | 4461 +++++++++++++++++ pyproject.toml | 178 +- studio/config/docker/Dockerfile | 10 +- studio/config/docker/Dockerfile.dev | 6 +- studio/config/docker/Dockerfile.test | 6 +- 10 files changed, 4567 insertions(+), 112 deletions(-) create mode 100644 poetry.lock diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml index 144a50985..f00109fe7 100644 --- a/docker-compose.dev.yml +++ b/docker-compose.dev.yml @@ -10,7 +10,7 @@ services: - .:/app ports: - "127.0.0.1:8000:8000" - command: python main.py --reload --host 0.0.0.0 --port 8000 + command: bash -c "poetry install --with dev && poetry run python main.py --reload --host 0.0.0.0 --port 8000" environment: PYTHONPATH: /app/ TZ: Asia/Tokyo diff --git a/docker-compose.test.yml b/docker-compose.test.yml index 8db6ab202..0db6d0c29 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -10,11 +10,9 @@ services: environment: PYTHONPATH: . TZ: Asia/Tokyo + command: bash -c "poetry install --with test && poetry run python3 -m pytest -s ." volumes: - - ./studio:/app/studio - - ./conda/yaml:/app/conda/yaml - - ./studio/test_data:/tmp/studio - - ./frontend/build:/app/frontend/build + - .:/app test_studio_frontend: image: test_studio_frontend diff --git a/docker-compose.yml b/docker-compose.yml index f83d298b6..de2d341b6 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -12,7 +12,7 @@ services: - ../optinist-docker-volumes/studio_data/:/app/studio_data ports: - "127.0.0.1:8000:8000" - command: python main.py --host 0.0.0.0 --port 8000 + command: poetry run python main.py --host 0.0.0.0 --port 8000 environment: PYTHONPATH: /app/ TZ: Asia/Tokyo diff --git a/docs/installation/each_platforms_for_developer.md b/docs/installation/each_platforms_for_developer.md index 219b9b4bf..227df339d 100644 --- a/docs/installation/each_platforms_for_developer.md +++ b/docs/installation/each_platforms_for_developer.md @@ -49,7 +49,7 @@ cd ./optinist ### Create anaconda environment ``` -conda create -n optinist_dev python=3.8 +conda create -n optinist_dev python=3.8 poetry conda activate optinist_dev ``` @@ -60,7 +60,7 @@ conda config --set channel_priority strict ### Install requirements ``` -pip install -e '.[dev]' +poetry install --with dev ``` If you will make PRs, please see the [](Contributing) section. diff --git a/docs/installation/each_platforms_for_developer_use_mamba.md b/docs/installation/each_platforms_for_developer_use_mamba.md index 00415a4bb..2611ced56 100644 --- a/docs/installation/each_platforms_for_developer_use_mamba.md +++ b/docs/installation/each_platforms_for_developer_use_mamba.md @@ -78,7 +78,7 @@ mamba create -c conda-forge -c bioconda -n optinist_dev python=3.8 snakemake --> ``` -mamba create -n optinist_dev python=3.8 +mamba create -n optinist_dev python=3.8 poetry conda activate optinist_dev ``` @@ -93,7 +93,7 @@ conda config --set channel_priority strict ### Install requirements ``` -pip 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"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 = "^3.8.1" +content-hash = "848368b68f1b8d48f6c2ffbc7f0cc0d678a51c5a79be7eeb21d1d4ae6299d1a3" diff --git a/pyproject.toml b/pyproject.toml index 8cb305a6d..e857fe7b4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,18 +1,14 @@ -[build-system] -requires = ["setuptools"] -build-backend = "setuptools.build_meta" - -[project] +[tool.poetry] name = "optinist" description = "Calcium Imaging Pipeline Tool" version = "1.0.1" +license = "GPL-3.0" +authors = ["OIST "] readme = "README.md" -requires-python = "==3.8.*" -license = {file = "LICENSE"} -authors = [ - {name = "OIST"}, -] -classifiers=[ +documentation = "https://optinist.readthedocs.io" +repository = "https://github.com/oist/optinist" +keywords = ["optinist"] +classifiers = [ "Intended Audience :: Developers", "Intended Audience :: Education", "Intended Audience :: Science/Research", @@ -24,98 +20,94 @@ classifiers=[ "Operating System :: Microsoft :: Windows", "Operating System :: MacOS :: MacOS X", ] -dependencies = [ - "fastapi==0.99.*", - "uvicorn==0.22.*", - "numpy>=1.23,<1.26", - "aiofiles", - "tqdm", - "pyyaml", - "imageio", - "tifffile", - "python-multipart", - "future", - "pynwb==2.2.0", - "psutil", - "nbstripout", - "snakemake>=7.24,<7.31", - "jinja2==3.1.*", - "httpx", - "firebase_admin", - "pyrebase4==4.7.1", - "pydantic[email]", - "pydantic[dotenv]", - "python-jose[cryptography]", - "alembic==1.9.2", - "sqlmodel==0.0.8", - "pymysql==1.0.2", - "fastapi_pagination==0.12.5", - "plotly==5.15.0", - "kaleido==0.2.1", - "filelock", -] +packages = [{ include = "studio" }] -[project.optional-dependencies] -dev = [ - "black", - "flake8==6.1.*", - "isort", - "build", - "twine", - "pre-commit", -] -doc = [ - "sphinx==7.1.2", - "sphinxcontrib-apidoc", - "sphinx_rtd_theme", - "sphinx-prompt", - "sphinx-pyproject", - "sphinx-autodoc-typehints", - "sphinx-copybutton==0.5.2", - "sphinx-autobuild==2021.3.14", - "myst-parser", -] -test = [ - "pytest", - "pytest-env", +include = [ + "frontend/build/*", + "frontend/build/static/*", + "frontend/build/static/css/*", + "frontend/build/static/js/*", + "frontend/build/static/media/*", + "studio/app/optinist/core/nwb/nwb.yaml", + "studio/app/common/core/snakemake/snakemake.yaml", + "studio/app/*/wrappers/**/*.yaml", + "studio/app/Snakefile", + "studio/config/*.yaml", ] +exclude = ["studio/tests/*", "conda.env.*"] -[project.urls] -Documentation = "https://optinist.readthedocs.io" -Repository = "https://github.com/oist/optinist" +[tool.poetry.dependencies] +python = "^3.8.1" +fastapi = "0.99.*" +uvicorn = "0.22.*" +numpy = { version = ">=1.23, <1.26" } +aiofiles = "*" +tqdm = "*" +pyyaml = "*" +imageio = "*" +tifffile = "*" +python-multipart = "*" +future = "*" +pynwb = "2.2.0" +psutil = "*" +nbstripout = "*" +snakemake = { version = 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"app/optinist/core/nwb/nwb.yaml", - "app/common/core/snakemake/snakemake.yaml", - "app/*/wrappers/**/*.yaml", - "app/Snakefile", - "config/*.yaml", -] +[tool.poetry.group.doc.dependencies] +sphinx = "7.1.2" +sphinxcontrib-apidoc = "*" +sphinx-rtd-theme = "*" +sphinx-prompt = "*" +sphinx-pyproject = "*" +sphinx-autodoc-typehints = "*" +sphinx-copybutton = "0.5.2" +sphinx-autobuild = "2021.3.14" +myst-parser = "*" + +[tool.poetry.group.test] +optional = true + +[tool.poetry.group.test.dependencies] +pytest = "*" +pytest-env = "*" + +[tool.poetry.scripts] +run_optinist = "studio.__main__:main" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" [tool.isort] profile = "black" [tool.pytest.ini_options] pythonpath = "." -env = [ - "OPTINIST_DIR=studio/test_data", -] +env = ["OPTINIST_DIR=studio/test_data"] diff --git a/studio/config/docker/Dockerfile b/studio/config/docker/Dockerfile index dd2818cc4..1d039ee56 100644 --- a/studio/config/docker/Dockerfile +++ b/studio/config/docker/Dockerfile @@ -19,11 +19,15 @@ RUN mkdir -p /root/miniconda3 && \ ENV PATH $PATH:/root/miniconda3/bin COPY frontend/build /app/frontend/build -COPY studio /app/studio -COPY main.py pyproject.toml ./ RUN pip3 install --no-cache-dir --upgrade pip && \ - pip3 install --no-cache-dir -e . + pip3 install poetry + +COPY main.py pyproject.toml poetry.lock ./ + +RUN poetry install --no-root + +COPY studio /app/studio RUN echo 'alias ll="ls -la"' >> ~/.bashrc RUN echo 'set nu ic hls nowrap ts=4 sw=4 | syntax on' >> ~/.vimrc diff --git a/studio/config/docker/Dockerfile.dev b/studio/config/docker/Dockerfile.dev index 8885c1405..aa2d90d5e 100644 --- a/studio/config/docker/Dockerfile.dev +++ b/studio/config/docker/Dockerfile.dev @@ -17,10 +17,10 @@ RUN mkdir -p /root/miniconda3 && \ ENV PATH $PATH:/root/miniconda3/bin -COPY pyproject.toml . - RUN pip3 install --no-cache-dir --upgrade pip && \ - pip3 install --no-cache-dir -e '.[dev]' + pip3 install poetry + +COPY pyproject.toml poetry.lock ./ RUN echo 'alias ll="ls -la"' >> ~/.bashrc RUN echo 'set nu ic hls nowrap ts=4 sw=4 | syntax on' >> ~/.vimrc diff --git a/studio/config/docker/Dockerfile.test b/studio/config/docker/Dockerfile.test index 960fc2734..a60738799 100644 --- a/studio/config/docker/Dockerfile.test +++ b/studio/config/docker/Dockerfile.test @@ -6,8 +6,8 @@ RUN apt-get --allow-releaseinfo-change update && \ apt-get install --no-install-recommends -y git gcc g++ libgl1 && \ apt-get purge git -y && apt-get autoremove -y && apt-get clean -COPY pyproject.toml . + RUN pip3 install --no-cache-dir --upgrade pip && \ - pip3 install --no-cache-dir -e '.[test]' + pip3 install poetry -ENTRYPOINT ["python3", "-m", "pytest", "-s", "."] +COPY pyproject.toml poetry.lock ./ From 22b9af6609d7de3e5957c61c3075747b936b225c Mon Sep 17 00:00:00 2001 From: quanpython Date: Mon, 6 Nov 2023 10:43:49 +0700 Subject: [PATCH 2/5] update poetry lock --- poetry.lock | 255 +++++++++++++++++++++++++------------------------ pyproject.toml | 1 + 2 files changed, 129 insertions(+), 127 deletions(-) diff --git a/poetry.lock b/poetry.lock index 66364607b..ac57bf4a0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -162,27 +162,26 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "build" -version = "1.0.3" +version = "0.10.0" description = "A simple, correct Python build frontend" category = "dev" optional = false python-versions = ">= 3.7" files = [ - {file = "build-1.0.3-py3-none-any.whl", hash = "sha256:589bf99a67df7c9cf07ec0ac0e5e2ea5d4b37ac63301c4986d1acb126aa83f8f"}, - {file = "build-1.0.3.tar.gz", hash = "sha256:538aab1b64f9828977f84bc63ae570b060a8ed1be419e7870b8b4fc5e6ea553b"}, + {file = "build-0.10.0-py3-none-any.whl", hash = "sha256:af266720050a66c893a6096a2f410989eeac74ff9a68ba194b3f6473e8e26171"}, + {file = "build-0.10.0.tar.gz", hash = "sha256:d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269"}, ] [package.dependencies] colorama = 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that supports roundtrip preservation of comments, seq/map flow style, and map key order" category = "main" optional = false -python-versions = ">=3" +python-versions = ">=3.7" files = [ - {file = "ruamel.yaml-0.18.4-py3-none-any.whl", hash = "sha256:ca864776af7b0cbcbb223c38707a440bfabea926ba5b4163b2ef4991aae8f8c1"}, - {file = "ruamel.yaml-0.18.4.tar.gz", hash = "sha256:a2778930d2573358f7c43f26e4bd5715015dccebf53c9943ed611200c1e2adcd"}, + {file = "ruamel.yaml-0.18.5-py3-none-any.whl", hash = "sha256:a013ac02f99a69cdd6277d9664689eb1acba07069f912823177c5eced21a6ada"}, + {file = "ruamel.yaml-0.18.5.tar.gz", hash = "sha256:61917e3a35a569c1133a8f772e1226961bf5a1198bea7e23f06a0841dea1ab0e"}, ] [package.dependencies] @@ -4458,4 +4459,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.8.1" -content-hash = "848368b68f1b8d48f6c2ffbc7f0cc0d678a51c5a79be7eeb21d1d4ae6299d1a3" +content-hash = "ef5fc33a61fe79ad20ec0e2a3cb9831598544f6915bafb82818a4686225b1527" diff --git a/pyproject.toml b/pyproject.toml index e857fe7b4..43fc039f7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -65,6 +65,7 @@ fastapi_pagination = "0.12.5" plotly = "5.15.0" kaleido = "0.2.1" filelock = "*" +ruamel-yaml = "^0.18.5" [tool.poetry.group.dev] optional = true From 908d2606ba7857410a8d4c51faba9a18c0818397 Mon Sep 17 00:00:00 2001 From: quanpython Date: Mon, 6 Nov 2023 19:47:01 +0700 Subject: [PATCH 3/5] poetry add `--no-root` options --- docker-compose.dev.yml | 2 +- docker-compose.test.yml | 2 +- docs/installation/each_platforms_for_developer.md | 2 +- docs/installation/each_platforms_for_developer_use_mamba.md | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml index f00109fe7..611d6350c 100644 --- a/docker-compose.dev.yml +++ b/docker-compose.dev.yml @@ -10,7 +10,7 @@ services: - .:/app ports: - "127.0.0.1:8000:8000" - command: bash -c "poetry install --with dev && poetry run python main.py --reload --host 0.0.0.0 --port 8000" + command: bash -c "poetry install --no-root --with dev && poetry run python main.py --reload --host 0.0.0.0 --port 8000" environment: PYTHONPATH: /app/ TZ: Asia/Tokyo diff --git a/docker-compose.test.yml b/docker-compose.test.yml index 0db6d0c29..1eceaa222 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -10,7 +10,7 @@ services: environment: PYTHONPATH: . TZ: Asia/Tokyo - command: bash -c "poetry install --with test && poetry run python3 -m pytest -s ." + command: bash -c "poetry install --no-root --with test && poetry run python3 -m pytest -s ." volumes: - .:/app diff --git a/docs/installation/each_platforms_for_developer.md b/docs/installation/each_platforms_for_developer.md index 227df339d..8c479fa26 100644 --- a/docs/installation/each_platforms_for_developer.md +++ b/docs/installation/each_platforms_for_developer.md @@ -60,7 +60,7 @@ conda config --set channel_priority strict ### Install requirements ``` -poetry install --with dev +poetry install --no-root --with dev ``` If you will make PRs, please see the [](Contributing) section. diff --git a/docs/installation/each_platforms_for_developer_use_mamba.md b/docs/installation/each_platforms_for_developer_use_mamba.md index 2611ced56..a4f8c82e8 100644 --- a/docs/installation/each_platforms_for_developer_use_mamba.md +++ b/docs/installation/each_platforms_for_developer_use_mamba.md @@ -93,7 +93,7 @@ conda config --set channel_priority strict ### Install requirements ``` -poetry install --with dev +poetry install --no-root --with dev ``` ### Set saving directory From 35c13ddba7d61ce70ad7299f5021acd1d6831d95 Mon Sep 17 00:00:00 2001 From: ReiHashimoto <42664619+ReiHashimoto@users.noreply.github.com> Date: Wed, 8 Nov 2023 16:41:54 +0900 Subject: [PATCH 4/5] remove sphinx-pyproject --- docs/conf.py | 5 +-- docs/requirements.txt | 1 - poetry.lock | 97 +++++++------------------------------------ pyproject.toml | 1 - 4 files changed, 16 insertions(+), 88 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 32269f2ea..05b23baf1 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -7,8 +7,6 @@ import os from datetime import datetime -from sphinx_pyproject import SphinxConfig - # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, @@ -18,11 +16,10 @@ # -- Project information ----------------------------------------------------- -config = SphinxConfig("../pyproject.toml", globalns=globals()) project = "OptiNiSt" copyright = f"{datetime.today().year}, OIST" author = "" -release = ".".join(config.version.split(".")[:2]) +release = "1.0.1" # -- readthedocs ------------------------------------------------------------- on_rtd = os.environ.get("READTHEDOCS", None) == "True" diff --git a/docs/requirements.txt b/docs/requirements.txt index ed1f751a9..c91811b04 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -6,4 +6,3 @@ sphinx-autodoc-typehints sphinx-copybutton==0.5.2 sphinx-autobuild==2021.3.14 myst-parser -sphinx-pyproject diff --git a/poetry.lock b/poetry.lock index ac57bf4a0..72f86b907 100644 --- a/poetry.lock +++ b/poetry.lock @@ -603,43 +603,6 @@ files = [ {file = "docutils-0.20.1.tar.gz", hash = "sha256:f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b"}, ] -[[package]] -name = "dom-toml" -version = "0.6.1" 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