From 1b0ccf641cb07aea003e1c2971e063fa05abc78d Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 1 Nov 2017 09:42:23 -0400 Subject: [PATCH] Use pipenv to generate development dependencies. - Rework pattern for linting dependencies to work for dev-requirements.txt. - Get rid of dev-requirements.txt and replace it with a symbolic link to the latest pinned versions of dependencies. Rebased against dev to bring in @nsoranzo's bashism bashings in #4876 and fixed up to strip trailing whitespace from generated requirement files. --- .ci/tox_envs/update.sh | 15 - Makefile | 7 +- lib/galaxy/dependencies/dev-requirements.txt | 18 +- .../dependencies/pipfiles/develop/Pipfile | 25 ++ .../pipfiles/develop/Pipfile.lock | 326 ++++++++++++++++++ .../develop/pinned-hashed-requirements.txt | 35 ++ .../pipfiles/develop/pinned-requirements.txt | 35 ++ .../dependencies/pipfiles}/flake8/Pipfile | 0 .../dependencies/pipfiles/flake8/Pipfile.lock | 77 +++++ .../flake8/pinned-hashed-requirements.txt | 0 .../pipfiles/flake8/pinned-requirements.txt | 6 + .../pipfiles}/flake8_imports/Pipfile | 0 .../pipfiles/flake8_imports/Pipfile.lock | 98 ++++++ .../pinned-hashed-requirements.txt | 0 .../flake8_imports/pinned-requirements.txt | 9 + lib/galaxy/dependencies/pipfiles/update.sh | 53 +++ tox.ini | 16 +- 17 files changed, 678 insertions(+), 42 deletions(-) delete mode 100755 .ci/tox_envs/update.sh mode change 100644 => 120000 lib/galaxy/dependencies/dev-requirements.txt create mode 100644 lib/galaxy/dependencies/pipfiles/develop/Pipfile create mode 100644 lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock create mode 100644 lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt create mode 100644 lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt rename {.ci/tox_envs => lib/galaxy/dependencies/pipfiles}/flake8/Pipfile (100%) create mode 100644 lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock rename .ci/tox_envs/flake8/requirements.txt => lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt (100%) create mode 100644 lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt rename {.ci/tox_envs => lib/galaxy/dependencies/pipfiles}/flake8_imports/Pipfile (100%) create mode 100644 lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock rename .ci/tox_envs/flake8_imports/requirements.txt => lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt (100%) create mode 100644 lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt create mode 100755 lib/galaxy/dependencies/pipfiles/update.sh diff --git a/.ci/tox_envs/update.sh b/.ci/tox_envs/update.sh deleted file mode 100755 index ebaecf980ea..00000000000 --- a/.ci/tox_envs/update.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/sh - -THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)" -ENVS="flake8 -flake8_imports" - -for env in $ENVS -do - cd "$THIS_DIRECTORY/$env" - pipenv lock - pipenv lock -r > requirements.txt -done - -git add -u "$THIS_DIRECTORY" -git commit -m "Rev and re-lock linting dependencies." diff --git a/Makefile b/Makefile index 7031b448297..a7c7787741a 100644 --- a/Makefile +++ b/Makefile @@ -119,8 +119,11 @@ release-check-blocking-prs: ## Check github for release blocking PRs release-bootstrap-history: ## bootstrap history for a new release $(IN_VENV) python scripts/bootstrap_history.py --release $(RELEASE_CURR) -update-linting-requirements: ## update linting dependencies - sh .ci/tox_envs/update.sh +update-dependencies: ## update linting + dev dependencies + sh lib/galaxy/dependencies/pipfiles/update.sh + +update-and-commit-dependencies: ## update and commit linting + dev dependencies + sh lib/galaxy/dependencies/pipfiles/update.sh -c node-deps: ## Install NodeJS dependencies. cd client && yarn install --check-files diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt deleted file mode 100644 index 7935fa71e59..00000000000 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ /dev/null @@ -1,17 +0,0 @@ -# For tests -nose -NoseHTML -twill==0.9.1 -testfixtures -mock -selenium -watchdog - -# For relase process -pygithub3 - -# For documentation building -sphinx -sphinx_rtd_theme -lxml -recommonmark diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt new file mode 120000 index 00000000000..8051686e764 --- /dev/null +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -0,0 +1 @@ +pipfiles/develop/pinned-requirements.txt \ No newline at end of file diff --git a/lib/galaxy/dependencies/pipfiles/develop/Pipfile b/lib/galaxy/dependencies/pipfiles/develop/Pipfile new file mode 100644 index 00000000000..7f13cc074a7 --- /dev/null +++ b/lib/galaxy/dependencies/pipfiles/develop/Pipfile @@ -0,0 +1,25 @@ +[[source]] + +url = "https://wheels.galaxyproject.org/simple" +verify_ssl = true +name = "galaxy" + +[[source]] + +url = "https://pypi.python.org/simple" +verify_ssl = true +name = "pypi" + +[packages] + +NoseHTML = "*" +twill = "==0.9.1" +mock = "*" +selenium = "*" +testfixtures = "*" +watchdog = "*" +"pygithub3" = "*" +Sphinx = "*" +sphinx_rtd_theme = "*" +lxml = "*" +recommonmark = "*" diff --git a/lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock b/lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock new file mode 100644 index 00000000000..800b6d1495a --- /dev/null +++ b/lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock @@ -0,0 +1,326 @@ +{ + "_meta": { + "hash": { + "sha256": "7da6298d5a5d49c87941125b449f37cc26c44d80f94d3d35a211463aa1efcf10" + }, + "host-environment-markers": { + "implementation_name": "cpython", + "implementation_version": "0", + "os_name": "posix", + "platform_machine": "x86_64", + "platform_python_implementation": "CPython", + "platform_release": "16.7.0", + "platform_system": "Darwin", + "platform_version": "Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64", + "python_full_version": "2.7.12", + "python_version": "2.7", + "sys_platform": "darwin" + }, + "pipfile-spec": 6, + "requires": {}, + "sources": [ + { + "name": "galaxy", + "url": "https://wheels.galaxyproject.org/simple", + "verify_ssl": true + }, + { + "name": "pypi", + "url": 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+watchdog==0.8.3 +lxml==4.1.0 +babel==2.5.1 +six==1.11.0 +selenium==3.6.0 +commonmark==0.5.4 +docutils==0.14 +typing==3.6.2; python_version < '3.5' +certifi==2017.7.27.1 +mock==2.0.0 +testfixtures==5.3.0 +imagesize==0.7.1 +alabaster==0.7.10 +urllib3==1.22 +argh==0.26.2 +markupsafe==1.0 +pytz==2017.3 +jinja2==2.9.6 +twill==0.9.1 +pygithub3==0.5.1 +pyyaml==3.12 +sphinx==1.6.5 +pbr==3.1.1 +sphinxcontrib-websupport==1.0.1 +pathtools==0.1.2 +sphinx-rtd-theme==0.2.4 +chardet==3.0.4 +nose==1.3.7 +requests==2.18.4 +idna==2.6 diff --git a/.ci/tox_envs/flake8/Pipfile b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile similarity index 100% rename from .ci/tox_envs/flake8/Pipfile rename to lib/galaxy/dependencies/pipfiles/flake8/Pipfile diff --git a/lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock new file mode 100644 index 00000000000..f45726344c0 --- /dev/null +++ b/lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock @@ -0,0 +1,77 @@ +{ + "_meta": { + "hash": { + "sha256": "23a9dc7e33425cf99801df781bf42cfb2ee9a72cfc8bbf725e1008ae543a821f" + }, + "host-environment-markers": { + "implementation_name": "cpython", + "implementation_version": "0", + "os_name": "posix", + "platform_machine": "x86_64", + "platform_python_implementation": "CPython", + "platform_release": "16.7.0", + "platform_system": "Darwin", + "platform_version": "Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64", + "python_full_version": "2.7.12", + "python_version": "2.7", + "sys_platform": "darwin" + }, + "pipfile-spec": 6, + "requires": {}, + "sources": [ + { + "name": "pypi", + "url": "https://pypi.python.org/simple", + "verify_ssl": true + } + ] + }, + "default": { + "configparser": { + "hashes": [ + "sha256:5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a" + ], + "markers": "python_version < '3.2'", + "version": "==3.5.0" + }, + "enum34": { + "hashes": [ + "sha256:6bd0f6ad48ec2aa117d3d141940d484deccda84d4fcd884f5c3d93c23ecd8c79", + "sha256:644837f692e5f550741432dd3f223bbb9852018674981b1664e5dc339387588a", + "sha256:8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1", + "sha256:2d81cbbe0e73112bdfe6ef8576f2238f2ba27dd0d55752a776c41d38b7da2850" + ], + "markers": "python_version < '3.4'", + "version": "==1.1.6" + }, + "flake8": { + "hashes": [ + "sha256:c7841163e2b576d435799169b78703ad6ac1bbb0f199994fc05f700b2a90ea37", + "sha256:7253265f7abd8b313e3892944044a365e3f4ac3fcdcfb4298f55ee9ddf188ba0" + ], + "version": "==3.5.0" + }, + "mccabe": { + "hashes": [ + "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42", + "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f" + ], + "version": "==0.6.1" + }, + "pycodestyle": { + "hashes": [ + "sha256:6c4245ade1edfad79c3446fadfc96b0de2759662dc29d07d80a6f27ad1ca6ba9", + "sha256:682256a5b318149ca0d2a9185d365d8864a768a28db66a84a2ea946bcc426766" + ], + "version": "==2.3.1" + }, + "pyflakes": { + "hashes": [ + "sha256:08bd6a50edf8cffa9fa09a463063c425ecaaf10d1eb0335a7e8b1401aef89e6f", + "sha256:8d616a382f243dbf19b54743f280b80198be0bca3a5396f1d2e1fca6223e8805" + ], + "version": "==1.6.0" + } + }, + "develop": {} +} diff --git a/.ci/tox_envs/flake8/requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt similarity index 100% rename from .ci/tox_envs/flake8/requirements.txt rename to lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt diff --git a/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt new file mode 100644 index 00000000000..23f41e35bc4 --- /dev/null +++ b/lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt @@ -0,0 +1,6 @@ +mccabe==0.6.1 +pycodestyle==2.3.1 +pyflakes==1.6.0 +enum34==1.1.6; python_version < '3.4' +flake8==3.5.0 +configparser==3.5.0; python_version < '3.2' diff --git a/.ci/tox_envs/flake8_imports/Pipfile b/lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile similarity index 100% rename from .ci/tox_envs/flake8_imports/Pipfile rename to lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile diff --git a/lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock b/lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock new file mode 100644 index 00000000000..998b7c73a90 --- /dev/null +++ b/lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock @@ -0,0 +1,98 @@ +{ + "_meta": { + "hash": { + "sha256": "68f35c8c353b79ccfd80ad884f83009e2b196c6fe761fa91b01f3d3c6804bb93" + }, + "host-environment-markers": { + "implementation_name": "cpython", + "implementation_version": "0", + "os_name": "posix", + "platform_machine": "x86_64", + "platform_python_implementation": "CPython", + "platform_release": "16.7.0", + "platform_system": "Darwin", + "platform_version": "Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64", + "python_full_version": "2.7.12", + "python_version": "2.7", + "sys_platform": "darwin" + }, + "pipfile-spec": 6, + "requires": {}, + "sources": [ + { + "name": "pypi", + "url": "https://pypi.python.org/simple", + "verify_ssl": true + } + ] + }, + "default": { + "asttokens": { + "hashes": [ + "sha256:37d32633cdeaebfd171f548aa0e77cc863b0692a1e96dc93d49c997a8d655a1a", + "sha256:97f568e6eaf9a133850bd5370193ef10a459fc9fff0c8954e986a30b44415a88" + ], + "version": "==1.1.6" + }, + "configparser": { + "hashes": [ + "sha256:5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a" + ], + "markers": "python_version < '3.2'", + "version": "==3.5.0" + }, + "enum34": { + "hashes": [ + "sha256:6bd0f6ad48ec2aa117d3d141940d484deccda84d4fcd884f5c3d93c23ecd8c79", + "sha256:644837f692e5f550741432dd3f223bbb9852018674981b1664e5dc339387588a", + "sha256:8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1", + "sha256:2d81cbbe0e73112bdfe6ef8576f2238f2ba27dd0d55752a776c41d38b7da2850" + ], + "markers": "python_version < '3.4'", + "version": "==1.1.6" + }, + "flake8": { + "hashes": [ + "sha256:c7841163e2b576d435799169b78703ad6ac1bbb0f199994fc05f700b2a90ea37", + "sha256:7253265f7abd8b313e3892944044a365e3f4ac3fcdcfb4298f55ee9ddf188ba0" + ], + "version": "==3.5.0" + }, + "flake8-import-order": { + "hashes": [ + "sha256:3351e102c4702391ba86d2acf22a0b2170336288193714dcc245d1ab9f0548f0", + "sha256:905ca7059f20d7371eca3ceb493ef2d58f466b1e2e62fdaa582c6107ff7894e1" + ], + "version": "==0.14.2" + }, + "mccabe": { + "hashes": [ + "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42", + "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f" + ], + "version": "==0.6.1" + }, + "pycodestyle": { + "hashes": [ + "sha256:6c4245ade1edfad79c3446fadfc96b0de2759662dc29d07d80a6f27ad1ca6ba9", + "sha256:682256a5b318149ca0d2a9185d365d8864a768a28db66a84a2ea946bcc426766" + ], + "version": "==2.3.1" + }, + "pyflakes": { + "hashes": [ + "sha256:08bd6a50edf8cffa9fa09a463063c425ecaaf10d1eb0335a7e8b1401aef89e6f", + "sha256:8d616a382f243dbf19b54743f280b80198be0bca3a5396f1d2e1fca6223e8805" + ], + "version": "==1.6.0" + }, + "six": { + "hashes": [ + "sha256:832dc0e10feb1aa2c68dcc57dbb658f1c7e65b9b61af69048abc87a2db00a0eb", + "sha256:70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9" + ], + "version": "==1.11.0" + } + }, + "develop": {} +} diff --git a/.ci/tox_envs/flake8_imports/requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt similarity index 100% rename from .ci/tox_envs/flake8_imports/requirements.txt rename to lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt diff --git a/lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt new file mode 100644 index 00000000000..7e06cfc4a40 --- /dev/null +++ b/lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt @@ -0,0 +1,9 @@ +asttokens==1.1.6 +pyflakes==1.6.0 +enum34==1.1.6; python_version < '3.4' +flake8-import-order==0.14.2 +six==1.11.0 +mccabe==0.6.1 +pycodestyle==2.3.1 +flake8==3.5.0 +configparser==3.5.0; python_version < '3.2' diff --git a/lib/galaxy/dependencies/pipfiles/update.sh b/lib/galaxy/dependencies/pipfiles/update.sh new file mode 100755 index 00000000000..33a2130f499 --- /dev/null +++ b/lib/galaxy/dependencies/pipfiles/update.sh @@ -0,0 +1,53 @@ +#!/bin/sh + +commit=0 + +usage() { +cat << EOF +Usage: ${0##*/} [-c] + +Use pipenv to regenerate locked and hashed versions of Galaxy dependencies. +Use -c to automatically commit these changes (be sure you have no staged git +changes). + +EOF +} + +while getopts ":hc" opt; do + case "$opt" in + h) + usage + exit 0 + ;; + c) + commit=1 + ;; + '?') + usage >&2 + exit 1 + ;; + esac +done + +THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)" +cd "$THIS_DIRECTORY" +ENVS="develop +flake8 +flake8_imports" + +for env in $ENVS +do + cd "$env" + pipenv lock + pipenv lock -r > pinned-hashed-requirements.txt + # Strip out hashes and trailing whitespace for unhashed version + # of this requirements file. + sed 's/--hash[^[:space:]]*//g' pinned-hashed-requirements.txt | sed 's/[[:space:]]*$//' > pinned-requirements.txt + cd ".." +done + +if [ "$commit" -eq "1" ]; +then + git add -u . + git commit -m "Rev and re-lock Galaxy dependencies." +fi diff --git a/tox.ini b/tox.ini index 0c22801b794..701d9a80fe0 100644 --- a/tox.ini +++ b/tox.ini @@ -5,23 +5,23 @@ skipsdist = True [testenv:py27-lint] commands = bash .ci/flake8_wrapper.sh whitelist_externals = bash -deps = -r.ci/tox_envs/flake8/requirements.txt +deps = -rlib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt [testenv:py33-lint] commands = bash .ci/flake8_wrapper.sh whitelist_externals = bash -deps = -r.ci/tox_envs/flake8/requirements.txt +deps = -rlib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt [testenv:py34-lint] commands = bash .ci/flake8_wrapper.sh whitelist_externals = bash -deps = -r.ci/tox_envs/flake8/requirements.txt +deps = -rlib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt [testenv:py35-lint] commands = bash .ci/flake8_wrapper.sh whitelist_externals = bash -deps = -r.ci/tox_envs/flake8/requirements.txt +deps = -rlib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt [testenv:py27-unit] commands = bash run_tests.sh --no-create-venv -u @@ -41,13 +41,13 @@ deps = commands = bash .ci/flake8_wrapper.sh whitelist_externals = bash skip_install = True -deps = -r.ci/tox_envs/flake8_imports/requirements.txt +deps = -rlib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt [testenv:py27-lint-imports-include-list] commands = bash .ci/flake8_wrapper_imports.sh whitelist_externals = bash skip_install = True -deps = -r.ci/tox_envs/flake8_imports/requirements.txt +deps = -rlib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt [testenv:qunit] commands = bash run_tests.sh -q @@ -73,13 +73,13 @@ whitelist_externals = bash commands = bash .ci/flake8_wrapper_docstrings.sh --exclude whitelist_externals = bash skip_install = True -deps = -r.ci/tox_envs/flake8/requirements.txt +deps = -rlib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt [testenv:py27-lint-docstring-include-list] commands = bash .ci/flake8_wrapper_docstrings.sh --include whitelist_externals = bash skip_install = True -deps = -r.ci/tox_envs/flake8/requirements.txt +deps = -rlib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt [testenv:check-python-dependencies] commands = make list-dependency-updates # someday change exit code on this.