From 055ba3df4f3058bf9a53198d73992288edb57907 Mon Sep 17 00:00:00 2001 From: korikuzma Date: Thu, 27 Jan 2022 09:10:07 -0500 Subject: [PATCH 1/2] Install postgresql-devel in commands + separate out container commands --- .ebextensions/01_download_data.config | 35 +++++++++++++-------------- 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/.ebextensions/01_download_data.config b/.ebextensions/01_download_data.config index c4d924ee..03011261 100644 --- a/.ebextensions/01_download_data.config +++ b/.ebextensions/01_download_data.config @@ -1,51 +1,50 @@ -container_commands: - 01_export_eb_env_var: - test: test ! -d "/usr/local/share/seqrepo" - command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)" - - 02_install_awscli: +commands: + 01_install_postgresql_devel: + command: "yum install -y python-devel postgresql-devel" + 02_install_aws_cli: command: "yum install -y awscli" - 03_install_unzip: - test: test ! -d "/usr/local/share/seqrepo" command: "yum install -y unzip" + 04_export_eb_env_var: + command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)" - 05_refseq_gene_symbol_download: +container_commands: + 01_refseq_gene_symbol_download: test: test ! -f "./variation/data/refseq_gene_symbols.txt" command: "aws s3 cp s3://${AWS_BUCKET_NAME}/variation/refseq_gene_symbols.txt ./variation/data/refseq_gene_symbols.txt --region us-east-2" - 06_mane_grch38_refseq_download: + 02_mane_grch38_refseq_download: test: test ! -f "./variation/data/MANE.GRCh38.v0.93.summary.txt" command: "aws s3 cp s3://${AWS_BUCKET_NAME}/variation/MANE.GRCh38.v0.93.summary.txt ./variation/data/MANE.GRCh38.v0.93.summary.txt --region us-east-2" - 07_s3_download: + 03_s3_download: test: test ! -d "/usr/local/share/seqrepo" command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.zip --region us-east-2" - 08_unzip_seqrepo: + 04_unzip_seqrepo: test: test -f "/usr/local/share/seqrepo.zip" command: "unzip /usr/local/share/seqrepo.zip -d /usr/local/share" - 09_seqrepo_permission: + 05_seqrepo_permission: test: test -d "/usr/local/share/seqrepo" command: "chmod -R 777 /usr/local/share/seqrepo" - 10_macosx_permission: + 06_macosx_permission: test: test -d "/usr/local/share/__MACOSX" command: "chmod -R +wr /usr/local/share/__MACOSX" - 11_seqrepo_zip_permission: + 07_seqrepo_zip_permission: test: test -f "/usr/local/share/seqrepo.zip" command: "chmod +wr /usr/local/share/seqrepo.zip" - 12_remove_macosx: + 08_remove_macosx: test: test -d "/usr/local/share/__MACOSX" command: "rm -R /usr/local/share/__MACOSX" - 13_remove_seqrepo_zip: + 09_remove_seqrepo_zip: test: test -f "/usr/local/share/seqrepo.zip" command: "rm /usr/local/share/seqrepo.zip" - 14_data_permission: + 10_data_permission: test: test -d "/usr/local/share/seqrepo" command: "chmod -R +wrx /usr/local/share/seqrepo" From 307062174524f796446aff7520571064cb488f4d Mon Sep 17 00:00:00 2001 From: korikuzma Date: Thu, 27 Jan 2022 09:11:52 -0500 Subject: [PATCH 2/2] Add psycopg2-binary to dev packages --- Pipfile | 1 + requirements-dev.txt | 45 ++++++++++++++++++++++---------------------- requirements.txt | 42 ++++++++++++++++++++--------------------- setup.cfg | 7 +++++++ 4 files changed, 52 insertions(+), 43 deletions(-) diff --git a/Pipfile b/Pipfile index 1db27c89..da7b8c23 100644 --- a/Pipfile +++ b/Pipfile @@ -18,6 +18,7 @@ jupyter = "*" ipykernel = "*" twine = "*" matplotlib = "*" +psycopg2-binary = "*" [packages] hgvs = "*" diff --git a/requirements-dev.txt b/requirements-dev.txt index 81797954..a2e41545 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -13,7 +13,7 @@ anyio==3.5.0; python_full_version >= '3.6.2' appdirs==1.4.4 appnope==0.1.2; sys_platform == 'darwin' -argcomplete==2.0.0; python_version >= '3.6' +argcomplete==2.0.0; python_full_version >= '3.6.0' argh==0.26.2 argon2-cffi-bindings==21.2.0; python_version >= '3.6' argon2-cffi==21.3.0; python_version >= '3.6' @@ -24,21 +24,21 @@ babel==2.9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, backcall==0.2.0 beautifulsoup4==4.10.0; python_version >= '3.1' biocommons.seqrepo==0.6.5 -bioutils==0.5.5; python_version >= '3.6' +bioutils==0.5.5; python_full_version >= '3.6.0' black==21.12b0; python_full_version >= '3.6.2' bleach==4.1.0; python_version >= '3.6' boto3==1.20.44 -botocore==1.23.44; python_version >= '3.6' +botocore==1.23.44; python_full_version >= '3.6.0' bs4==0.0.1 canonicaljson==1.5.0; python_version ~= '3.5' certifi==2021.10.8 cffi==1.15.0 cfgv==3.3.1; python_full_version >= '3.6.1' charset-normalizer==2.0.10; python_version >= '3' -click==8.0.3; python_version >= '3.6' +click==8.0.3; python_full_version >= '3.6.0' colorama==0.4.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' coloredlogs==15.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -configparser==5.2.0; python_version >= '3.6' +configparser==5.2.0; python_full_version >= '3.6.0' coverage==6.3 coveralls==3.3.1 cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' @@ -57,13 +57,13 @@ filelock==3.4.2; python_version >= '3.7' flake8-docstrings==1.6.0 flake8==4.0.1 fonttools==4.29.0; python_version >= '3.7' -frozendict==2.2.0; python_version >= '3.6' +frozendict==2.2.1; python_full_version >= '3.6.0' ga4gh.vrs[extras]==0.7.2 ga4gh.vrsatile.pydantic==0.0.6 gene-normalizer==0.1.24 gffutils==0.10.1 greenlet==1.1.2; python_version >= '3' and platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32'))))) -h11==0.13.0; python_version >= '3.6' +h11==0.13.0; python_full_version >= '3.6.0' hgvs==1.5.2 httptools==0.3.0 humanfriendly==10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' @@ -76,7 +76,7 @@ ipykernel==6.7.0 ipython-genutils==0.2.0 ipython==8.0.1; python_version >= '3.8' ipywidgets==7.6.5 -jedi==0.18.1; python_version >= '3.6' +jedi==0.18.1; python_full_version >= '3.6.0' jinja2==3.0.3; python_version >= '3.6' jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3' json5==0.9.6 @@ -93,7 +93,7 @@ jupyterlab==3.2.8 keyring==23.5.0; python_version >= '3.7' kiwisolver==1.3.2; python_version >= '3.7' lxml==4.7.1 -markdown==3.3.6; python_version >= '3.6' +markdown==3.3.6; python_full_version >= '3.6.0' markupsafe==2.0.1; python_version >= '3.6' matplotlib-inline==0.1.3; python_version >= '3.5' matplotlib==3.5.1 @@ -107,13 +107,13 @@ nbformat==5.1.3; python_version >= '3.5' nest-asyncio==1.5.4; python_version >= '3.5' nodeenv==1.6.0 notebook==6.4.8; python_version >= '3.6' -numpy==1.22.1; python_version < '3.10' and platform_machine != 'aarch64' and platform_machine != 'arm64' +numpy==1.22.1; python_version >= '3.8' packaging==21.3; python_version >= '3.6' pandas==1.4.0 pandocfilters==1.5.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' parse==1.19.0 parsley==1.3 -parso==0.8.3; python_version >= '3.6' +parso==0.8.3; python_full_version >= '3.6.0' pathspec==0.9.0 pexpect==4.8.0; sys_platform != 'win32' pickleshare==0.7.5 @@ -123,8 +123,9 @@ platformdirs==2.4.1; python_version >= '3.7' pluggy==1.0.0; python_version >= '3.6' pre-commit==2.17.0 prometheus-client==0.13.0; python_version >= '3.6' -prompt-toolkit==3.0.24; python_full_version >= '3.6.2' -psycopg2==2.9.3; python_version >= '3.6' +prompt-toolkit==3.0.25; python_full_version >= '3.6.2' +psycopg2-binary==2.9.3 +psycopg2==2.9.3; python_full_version >= '3.6.0' ptyprocess==0.7.0 pure-eval==0.2.2 py==1.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' @@ -138,7 +139,7 @@ pyflakes==2.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3. pygments==2.11.2; python_version >= '3.5' pyliftover==0.4 pyparsing==3.0.7; python_version >= '3.6' -pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0' +pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4' pyquery==1.4.3 pyrsistent==0.18.1; python_version >= '3.7' pysam==0.18.0 @@ -147,38 +148,38 @@ pytest==6.2.5 python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' python-jsonschema-objects==0.4.1 pytz==2021.3 -pyyaml==6.0; python_version >= '3.6' +pyyaml==6.0; python_full_version >= '3.6.0' pyzmq==22.3.0; python_version >= '3.6' qtconsole==5.2.2; python_version >= '3.6' qtpy==2.0.0; python_version >= '3.6' readme-renderer==32.0; python_version >= '3.6' -requests-html==0.10.0; python_version >= '3.6' +requests-html==0.10.0; python_full_version >= '3.6.0' requests-toolbelt==0.9.1 requests==2.27.1 rfc3986==2.0.0; python_version >= '3.7' -s3transfer==0.5.0; python_version >= '3.6' +s3transfer==0.5.0; python_full_version >= '3.6.0' send2trash==1.8.0 setuptools==60.5.0; python_version >= '3.7' simplejson==3.17.6; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3' six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' sniffio==1.2.0; python_version >= '3.5' snowballstemmer==2.2.0 -soupsieve==2.3.1; python_version >= '3.6' +soupsieve==2.3.1; python_full_version >= '3.6.0' sqlalchemy==1.4.31 sqlparse==0.4.2; python_version >= '3.5' stack-data==0.1.4 -starlette==0.17.1; python_version >= '3.6' +starlette==0.17.1; python_full_version >= '3.6.0' tabulate==0.8.9 -terminado==0.12.1; python_version >= '3.6' +terminado==0.13.0; python_version >= '3.6' testpath==0.5.0; python_version >= '3.5' toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3' -tomli==1.2.3; python_version >= '3.6' +tomli==1.2.3; python_full_version >= '3.6.0' tornado==6.1; python_version >= '3.5' tqdm==4.62.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' traitlets==5.1.1; python_version >= '3.7' twine==3.7.1 typing-extensions==4.0.1 -urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4.0' +urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4' uvicorn==0.17.0.post1 uvloop==0.16.0 virtualenv==20.13.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' diff --git a/requirements.txt b/requirements.txt index d25c154c..4805ec1a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ anyio==3.5.0; python_full_version >= '3.6.2' appdirs==1.4.4 appnope==0.1.2; sys_platform == 'darwin' -argcomplete==2.0.0; python_version >= '3.6' +argcomplete==2.0.0; python_full_version >= '3.6.0' argh==0.26.2 asgiref==3.5.0; python_version >= '3.7' asttokens==2.0.5 @@ -17,29 +17,29 @@ attrs==21.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, backcall==0.2.0 beautifulsoup4==4.10.0; python_version >= '3.1' biocommons.seqrepo==0.6.5 -bioutils==0.5.5; python_version >= '3.6' +bioutils==0.5.5; python_full_version >= '3.6.0' black==21.12b0; python_full_version >= '3.6.2' boto3==1.20.44 -botocore==1.23.44; python_version >= '3.6' +botocore==1.23.44; python_full_version >= '3.6.0' bs4==0.0.1 canonicaljson==1.5.0; python_version ~= '3.5' certifi==2021.10.8 charset-normalizer==2.0.10; python_version >= '3' -click==8.0.3; python_version >= '3.6' +click==8.0.3; python_full_version >= '3.6.0' coloredlogs==15.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' -configparser==5.2.0; python_version >= '3.6' +configparser==5.2.0; python_full_version >= '3.6.0' cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' decorator==5.1.1; python_version >= '3.5' executing==0.8.2 fake-useragent==0.1.11 fastapi==0.73.0 -frozendict==2.2.0; python_version >= '3.6' +frozendict==2.2.1; python_full_version >= '3.6.0' ga4gh.vrs[extras]==0.7.2 ga4gh.vrsatile.pydantic==0.0.6 gene-normalizer==0.1.24 gffutils==0.10.1 greenlet==1.1.2; python_version >= '3' and platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32'))))) -h11==0.13.0; python_version >= '3.6' +h11==0.13.0; python_full_version >= '3.6.0' hgvs==1.5.2 httptools==0.3.0 humanfriendly==10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' @@ -47,24 +47,24 @@ idna==3.3; python_version >= '3' importlib-metadata==4.10.1; python_version < '3.10' inflection==0.5.1; python_version >= '3.5' ipython==8.0.1; python_version >= '3.8' -jedi==0.18.1; python_version >= '3.6' +jedi==0.18.1; python_full_version >= '3.6.0' jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3' jsonschema==3.2.0 lxml==4.7.1 -markdown==3.3.6; python_version >= '3.6' +markdown==3.3.6; python_full_version >= '3.6.0' matplotlib-inline==0.1.3; python_version >= '3.5' mypy-extensions==0.4.3 -numpy==1.22.1; python_version < '3.10' and platform_machine != 'aarch64' and platform_machine != 'arm64' +numpy==1.22.1; python_version >= '3.8' pandas==1.4.0 parse==1.19.0 parsley==1.3 -parso==0.8.3; python_version >= '3.6' +parso==0.8.3; python_full_version >= '3.6.0' pathspec==0.9.0 pexpect==4.8.0; sys_platform != 'win32' pickleshare==0.7.5 platformdirs==2.4.1; python_version >= '3.7' -prompt-toolkit==3.0.24; python_full_version >= '3.6.2' -psycopg2==2.9.3; python_version >= '3.6' +prompt-toolkit==3.0.25; python_full_version >= '3.6.2' +psycopg2==2.9.3; python_full_version >= '3.6.0' ptyprocess==0.7.0 pure-eval==0.2.2 pydantic==1.9.0 @@ -72,32 +72,32 @@ pyee==8.2.2 pyfaidx==0.6.3.1 pygments==2.11.2; python_version >= '3.5' pyliftover==0.4 -pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0' +pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4' pyquery==1.4.3 pyrsistent==0.18.1; python_version >= '3.7' pysam==0.18.0 python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' python-jsonschema-objects==0.4.1 pytz==2021.3 -pyyaml==6.0; python_version >= '3.6' -requests-html==0.10.0; python_version >= '3.6' +pyyaml==6.0; python_full_version >= '3.6.0' +requests-html==0.10.0; python_full_version >= '3.6.0' requests==2.27.1 -s3transfer==0.5.0; python_version >= '3.6' +s3transfer==0.5.0; python_full_version >= '3.6.0' setuptools==60.5.0; python_version >= '3.7' simplejson==3.17.6; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3' six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' sniffio==1.2.0; python_version >= '3.5' -soupsieve==2.3.1; python_version >= '3.6' +soupsieve==2.3.1; python_full_version >= '3.6.0' sqlalchemy==1.4.31 sqlparse==0.4.2; python_version >= '3.5' stack-data==0.1.4 -starlette==0.17.1; python_version >= '3.6' +starlette==0.17.1; python_full_version >= '3.6.0' tabulate==0.8.9 -tomli==1.2.3; python_version >= '3.6' +tomli==1.2.3; python_full_version >= '3.6.0' tqdm==4.62.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3' traitlets==5.1.1; python_version >= '3.7' typing-extensions==4.0.1 -urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4.0' +urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4' uvicorn==0.17.0.post1 uvloop==0.16.0 w3lib==1.22.0 diff --git a/setup.cfg b/setup.cfg index 38b4d8b7..ade3ceec 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,5 +50,12 @@ variation = data/transcript_mapping.tsv +[options.extras_require] +dev = + pytest + pytest-cov + pyyaml + psycopg2-binary + [tool:pytest] addopts = --ignore setup.py --doctest-modules --cov-report term-missing --cov .