From 8079c969932d53bb43207f5799af648f931cd34a Mon Sep 17 00:00:00 2001
From: Norman Rzepka <norman.rzepka@scalableminds.com>
Date: Wed, 18 Dec 2019 10:24:25 +0100
Subject: [PATCH] Poetry (#175)

* use poetry instead of pip/setup.py
* install poetry
* docker
* mention setuptools-scm
* test publish
* ci
* ci
* Update main.yml
* ci
* Merge branch 'poetry' of github.com:scalableminds/webknossos-cuber into poetry
* publish
---
 .github/workflows/main.yml |  22 +-
 Dockerfile                 |  13 +-
 poetry.lock                | 801 +++++++++++++++++++++++++++++++++++++
 poetry.toml                |   2 +
 publish.sh                 |  12 +
 pyproject.toml             |  29 ++
 requirements.txt           |  13 -
 setup.py                   |  22 -
 test.sh                    |  36 +-
 9 files changed, 882 insertions(+), 68 deletions(-)
 create mode 100644 poetry.lock
 create mode 100644 poetry.toml
 create mode 100755 publish.sh
 create mode 100644 pyproject.toml
 delete mode 100644 requirements.txt
 delete mode 100644 setup.py

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 71dfc2cd5..e6ed9f8c3 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.7]
+        python-version: [3.6, 3.7]
 
     steps:
     - uses: actions/checkout@v1
@@ -22,7 +22,9 @@ jobs:
       run: docker build -t scalableminds/webknossos-cuber:$GITHUB_SHA .
 
     - name: Install dependencies
-      run: pip install -r requirements.txt
+      run: |
+        pip install poetry
+        poetry install
       
     - name: Decompress test data
       run: tar -xzvf testdata/WT1_wkw.tar.gz
@@ -122,12 +124,14 @@ jobs:
           docker push scalableminds/webknossos-cuber:latest
         fi
 
+    - name: Check if git is dirty
+      run: |
+        git diff --no-ext-diff --quiet --exit-code
+        [[ -z $(git status -s) ]]
+
     - name: Publish python package
-      if: startsWith(github.event.ref, 'refs/tags')
+      if: startsWith(github.event.ref, 'refs/tags') && matrix.python-version == '3.7'
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        pip install twine
-        python setup.py sdist
-        twine upload dist/*
+        PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: ./publish.sh
diff --git a/Dockerfile b/Dockerfile
index c0e29e77d..db84abb2b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,16 +2,17 @@ FROM python:3.7
 
 RUN mkdir /app
 WORKDIR /app
-COPY requirements.txt /app
-COPY setup.py /app
+
 COPY README.md /app
-RUN pip install -r requirements.txt
+COPY poetry.toml /app
+COPY poetry.lock /app
+COPY pyproject.toml /app
+
+RUN pip install poetry
 
 COPY wkcuber /app/wkcuber
 COPY tests /app/tests
 
-COPY .git /app/.git
-RUN python setup.py install
-RUN rm -r /app/.git
+RUN poetry install --no-dev
 
 ENTRYPOINT [ "python", "-m" ]
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 000000000..e56095003
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,801 @@
+[[package]]
+category = "dev"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+name = "appdirs"
+optional = false
+python-versions = "*"
+version = "1.4.3"
+
+[[package]]
+category = "dev"
+description = "An abstract syntax tree for Python with inference support."
+name = "astroid"
+optional = false
+python-versions = ">=3.5.*"
+version = "2.3.3"
+
+[package.dependencies]
+lazy-object-proxy = ">=1.4.0,<1.5.0"
+six = ">=1.12,<2.0"
+wrapt = ">=1.11.0,<1.12.0"
+
+[package.dependencies.typed-ast]
+python = "<3.8"
+version = ">=1.4.0,<1.5"
+
+[[package]]
+category = "dev"
+description = "Atomic file writes."
+marker = "sys_platform == \"win32\""
+name = "atomicwrites"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "1.3.0"
+
+[[package]]
+category = "dev"
+description = "Classes Without Boilerplate"
+name = "attrs"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "19.3.0"
+
+[package.extras]
+azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "pytest-azurepipelines"]
+dev = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "pre-commit"]
+docs = ["sphinx", "zope.interface"]
+tests = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
+
+[[package]]
+category = "dev"
+description = "The uncompromising code formatter."
+name = "black"
+optional = false
+python-versions = ">=3.6"
+version = "19.3b0"
+
+[package.dependencies]
+appdirs = "*"
+attrs = ">=18.1.0"
+click = ">=6.5"
+toml = ">=0.9.4"
+
+[package.extras]
+d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
+
+[[package]]
+category = "main"
+description = "Python package for providing Mozilla's CA Bundle."
+name = "certifi"
+optional = false
+python-versions = "*"
+version = "2019.11.28"
+
+[[package]]
+category = "main"
+description = "Foreign Function Interface for Python calling C code."
+name = "cffi"
+optional = false
+python-versions = "*"
+version = "1.13.2"
+
+[package.dependencies]
+pycparser = "*"
+
+[[package]]
+category = "main"
+description = "Universal encoding detector for Python 2 and 3"
+name = "chardet"
+optional = false
+python-versions = "*"
+version = "3.0.4"
+
+[[package]]
+category = "dev"
+description = "Composable command line interface toolkit"
+name = "click"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "7.0"
+
+[[package]]
+category = "main"
+description = "Extended pickling support for Python objects"
+name = "cloudpickle"
+optional = false
+python-versions = "*"
+version = "1.2.2"
+
+[[package]]
+category = "main"
+description = "Utility library for easily distributing code execution on clusters"
+name = "cluster-tools"
+optional = false
+python-versions = "*"
+version = "1.46"
+
+[package.dependencies]
+cloudpickle = "*"
+
+[[package]]
+category = "dev"
+description = "Cross-platform colored terminal text."
+marker = "sys_platform == \"win32\""
+name = "colorama"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+version = "0.4.3"
+
+[[package]]
+category = "main"
+description = "Internationalized Domain Names in Applications (IDNA)"
+name = "idna"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "2.8"
+
+[[package]]
+category = "dev"
+description = "Read metadata from Python packages"
+marker = "python_version < \"3.8\""
+name = "importlib-metadata"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+version = "1.3.0"
+
+[package.dependencies]
+zipp = ">=0.5"
+
+[package.extras]
+docs = ["sphinx", "rst.linker"]
+testing = ["packaging", "importlib-resources"]
+
+[[package]]
+category = "dev"
+description = "A Python utility / library to sort Python imports."
+name = "isort"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "4.3.21"
+
+[package.extras]
+pipfile = ["pipreqs", "requirementslib"]
+pyproject = ["toml"]
+requirements = ["pipreqs", "pip-api"]
+xdg_home = ["appdirs (>=1.4.0)"]
+
+[[package]]
+category = "dev"
+description = "A fast and thorough lazy object proxy."
+name = "lazy-object-proxy"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "1.4.3"
+
+[[package]]
+category = "dev"
+description = "McCabe checker, plugin for flake8"
+name = "mccabe"
+optional = false
+python-versions = "*"
+version = "0.6.1"
+
+[[package]]
+category = "dev"
+description = "More routines for operating on iterables, beyond itertools"
+name = "more-itertools"
+optional = false
+python-versions = ">=3.5"
+version = "8.0.2"
+
+[[package]]
+category = "main"
+description = "Simple yet flexible natural sorting in Python."
+name = "natsort"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "6.2.0"
+
+[package.extras]
+fast = ["fastnumbers (>=2.0.0)"]
+icu = ["PyICU (>=1.0.0)"]
+
+[[package]]
+category = "main"
+description = "Access a multitude of neuroimaging data formats"
+name = "nibabel"
+optional = false
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
+version = "2.5.1"
+
+[package.dependencies]
+numpy = ">=1.8"
+six = ">=1.3"
+
+[package.extras]
+all = ["dicom (>=0.9.9)", "sphinx (>=0.3)", "nose (>=0.11)"]
+dicom = ["dicom (>=0.9.9)"]
+doc = ["sphinx (>=0.3)"]
+test = ["nose (>=0.11)"]
+
+[[package]]
+category = "main"
+description = "NumPy is the fundamental package for array computing with Python."
+name = "numpy"
+optional = false
+python-versions = ">=3.5"
+version = "1.17.4"
+
+[[package]]
+category = "dev"
+description = "Core utilities for Python packages"
+name = "packaging"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "19.2"
+
+[package.dependencies]
+pyparsing = ">=2.0.2"
+six = "*"
+
+[[package]]
+category = "main"
+description = "Python Imaging Library (Fork)"
+name = "pillow"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+version = "6.2.1"
+
+[[package]]
+category = "dev"
+description = "plugin and hook calling mechanisms for python"
+name = "pluggy"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "0.13.1"
+
+[package.dependencies]
+[package.dependencies.importlib-metadata]
+python = "<3.8"
+version = ">=0.12"
+
+[package.extras]
+dev = ["pre-commit", "tox"]
+
+[[package]]
+category = "main"
+description = "Cross-platform lib for process and system monitoring in Python."
+name = "psutil"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "5.6.7"
+
+[package.extras]
+enum = ["enum34"]
+
+[[package]]
+category = "dev"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+name = "py"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "1.8.0"
+
+[[package]]
+category = "main"
+description = "C parser in Python"
+name = "pycparser"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "2.19"
+
+[[package]]
+category = "dev"
+description = "python code static checker"
+name = "pylint"
+optional = false
+python-versions = ">=3.4.*"
+version = "2.3.1"
+
+[package.dependencies]
+astroid = ">=2.2.0,<3"
+colorama = "*"
+isort = ">=4.2.5,<5"
+mccabe = ">=0.6,<0.7"
+
+[[package]]
+category = "dev"
+description = "Python parsing module"
+name = "pyparsing"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+version = "2.4.5"
+
+[[package]]
+category = "dev"
+description = "pytest: simple powerful testing with Python"
+name = "pytest"
+optional = false
+python-versions = ">=3.5"
+version = "5.3.2"
+
+[package.dependencies]
+atomicwrites = ">=1.0"
+attrs = ">=17.4.0"
+colorama = "*"
+more-itertools = ">=4.0.0"
+packaging = "*"
+pluggy = ">=0.12,<1.0"
+py = ">=1.5.0"
+wcwidth = "*"
+
+[package.dependencies.importlib-metadata]
+python = "<3.8"
+version = ">=0.12"
+
+[package.extras]
+testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
+
+[[package]]
+category = "main"
+description = "YAML parser and emitter for Python"
+name = "pyyaml"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "5.2"
+
+[[package]]
+category = "main"
+description = "Python HTTP for Humans."
+name = "requests"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+version = "2.22.0"
+
+[package.dependencies]
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+urllib3 = ">=1.21.1,<1.25.0 || >1.25.0,<1.25.1 || >1.25.1,<1.26"
+
+[package.extras]
+security = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)"]
+socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"]
+
+[[package]]
+category = "main"
+description = "SciPy: Scientific Library for Python"
+name = "scipy"
+optional = false
+python-versions = ">=3.5"
+version = "1.4.0"
+
+[package.dependencies]
+numpy = ">=1.13.3"
+
+[[package]]
+category = "dev"
+description = "the blessed package to manage your versions by scm tags"
+name = "setuptools-scm"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+version = "3.3.3"
+
+[[package]]
+category = "main"
+description = "Python 2 and 3 compatibility utilities"
+name = "six"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*"
+version = "1.13.0"
+
+[[package]]
+category = "dev"
+description = "Python Library for Tom's Obvious, Minimal Language"
+name = "toml"
+optional = false
+python-versions = "*"
+version = "0.10.0"
+
+[[package]]
+category = "dev"
+description = "a fork of Python 2 and 3 ast modules with type comment support"
+marker = "implementation_name == \"cpython\" and python_version < \"3.8\""
+name = "typed-ast"
+optional = false
+python-versions = "*"
+version = "1.4.0"
+
+[[package]]
+category = "main"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+name = "urllib3"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4"
+version = "1.25.7"
+
+[package.extras]
+brotli = ["brotlipy (>=0.6.0)"]
+secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "ipaddress"]
+socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7,<2.0)"]
+
+[[package]]
+category = "dev"
+description = "Measures number of Terminal column cells of wide-character codes"
+name = "wcwidth"
+optional = false
+python-versions = "*"
+version = "0.1.7"
+
+[[package]]
+category = "main"
+description = ""
+name = "wkw"
+optional = false
+python-versions = "*"
+version = "0.1.2"
+
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+
+[[package]]
+category = "dev"
+description = "Module for decorators, wrappers and monkey patching."
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+optional = false
+python-versions = "*"
+version = "1.11.2"
+
+[[package]]
+category = "dev"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+marker = "python_version < \"3.8\""
+name = "zipp"
+optional = false
+python-versions = ">=2.7"
+version = "0.6.0"
+
+[package.dependencies]
+more-itertools = "*"
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"]
+testing = ["pathlib2", "contextlib2", "unittest2"]
+
+[metadata]
+content-hash = "fa3824bee7012c6b2f52d0972a77158fb0204c2dde9a12d8f0b0ec3030b13e16"
+python-versions = "^3.6"
+
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+]
+zipp = [
+    {file = "zipp-0.6.0-py2.py3-none-any.whl", hash = "sha256:f06903e9f1f43b12d371004b4ac7b06ab39a44adc747266928ae6debfa7b3335"},
+    {file = "zipp-0.6.0.tar.gz", hash = "sha256:3718b1cbcd963c7d4c5511a8240812904164b7f381b647143a89d3b98f9bcd8e"},
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diff --git a/poetry.toml b/poetry.toml
new file mode 100644
index 000000000..084377a03
--- /dev/null
+++ b/poetry.toml
@@ -0,0 +1,2 @@
+[virtualenvs]
+create = false
diff --git a/publish.sh b/publish.sh
new file mode 100755
index 000000000..366675cac
--- /dev/null
+++ b/publish.sh
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+set -eEuo pipefail
+set +x
+
+cp pyproject.toml pyproject.toml.bak
+PKG_VERSION=$(python -c "from setuptools_scm import get_version;print(get_version(),end='')")
+
+sed -i "0,/version = \".*\"/{s/version = \".*\"/version = \"$PKG_VERSION\"/}" pyproject.toml
+poetry publish --build -u $PYPI_USERNAME -p $PYPI_PASSWORD
+
+# Restore files
+mv pyproject.toml.bak pyproject.toml
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..a179e77d1
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,29 @@
+[tool.poetry]
+name = "wkcuber"
+version = "0.0.0" # filled by setuptools-scm
+description = "A cubing tool for webKnossos"
+authors = ["scalable minds <hello@scalableminds.com>"]
+license = "AGPL-3.0"
+
+[tool.poetry.dependencies]
+python = "^3.6"
+scipy = "^1.4.0"
+numpy = "^1.17.4"
+pillow = "^6.2.1"
+pyyaml = "^5.2"
+wkw = "0.1.2"
+requests = "^2.22.0"
+cluster_tools = "1.46"
+natsort = "^6.2.0"
+psutil = "^5.6.7"
+nibabel = "^2.5.1"
+
+[tool.poetry.dev-dependencies]
+pylint = "2.3.1"
+black = "19.3b0"
+pytest = "^5.3.2"
+setuptools-scm = "^3.3.3"
+
+[build-system]
+requires = ["poetry>=0.12"]
+build-backend = "poetry.masonry.api"
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index f45ec0234..000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-scipy
-numpy
-pillow
-pyyaml
-pytest
-wkw==0.1.2
-requests
-black==19.3b0
-cluster_tools==1.46
-natsort
-psutil
-nibabel
-pylint==2.3.1
\ No newline at end of file
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 4ed122b34..000000000
--- a/setup.py
+++ /dev/null
@@ -1,22 +0,0 @@
-from setuptools import setup, find_packages
-
-setup(
-    name="wkcuber",
-    packages=find_packages(exclude=("tests",)),
-    use_scm_version=True,
-    setup_requires=["setuptools_scm"],
-    install_requires=[
-        "scipy",
-        "numpy",
-        "pillow",
-        "pyyaml",
-        "wkw",
-        "psutil",
-        "cluster_tools==1.46",
-        "natsort",
-    ],
-    description="A cubing tool for webKnossos",
-    author="Norman Rzepka",
-    author_email="norman.rzepka@scalableminds.com",
-    url="https://scalableminds.com",
-)
diff --git a/test.sh b/test.sh
index 26a43112f..1519ab704 100755
--- a/test.sh
+++ b/test.sh
@@ -1,18 +1,18 @@
- export CIRCLE_BUILD_NUM=latest
- tests/scripts/build_docker_image.sh
- tests/scripts/decompress_test_data.sh
- tests/scripts/check_formatting.sh
- tests/scripts/python_tests.sh
- tests/scripts/tiff_cubing.sh
- tests/scripts/in_memory_downsampled_cubing.sh
- tests/scripts/tile_cubing.sh
- tests/scripts/simple_tiff_cubing.sh
- tests/scripts/simple_tiff_cubing_no_compression.sh
- tests/scripts/knossos_conversion.sh
- tests/scripts/decompress_reference_mag.sh
- tests/scripts/downsampling.sh
- tests/scripts/compression.sh
- tests/scripts/in_place_compression.sh
- tests/scripts/meta_generation.sh
- tests/scripts/simple_anisotropic_tiff_cubing.sh
- tests/scripts/anisotropic_downsampling.sh
\ No newline at end of file
+export CIRCLE_BUILD_NUM=latest
+tests/scripts/build_docker_image.sh
+tests/scripts/decompress_test_data.sh
+tests/scripts/check_formatting.sh
+tests/scripts/python_tests.sh
+tests/scripts/tiff_cubing.sh
+tests/scripts/in_memory_downsampled_cubing.sh
+tests/scripts/tile_cubing.sh
+tests/scripts/simple_tiff_cubing.sh
+tests/scripts/simple_tiff_cubing_no_compression.sh
+tests/scripts/knossos_conversion.sh
+tests/scripts/decompress_reference_mag.sh
+tests/scripts/downsampling.sh
+tests/scripts/compression.sh
+tests/scripts/in_place_compression.sh
+tests/scripts/meta_generation.sh
+tests/scripts/simple_anisotropic_tiff_cubing.sh
+tests/scripts/anisotropic_downsampling.sh
\ No newline at end of file