From dcf1cae74919a169640252beed2cb7f7ebc7bddd Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Thu, 16 Jun 2022 16:57:40 +0200 Subject: [PATCH] refactor: move requirements/ to code/requirements/ --- .github/workflows/memote-history.yml | 2 +- .github/workflows/memote-run.yml | 2 +- .github/workflows/memote_release.yml | 2 +- .github/workflows/yaml-validation.yml | 2 +- README.md | 2 +- .../requirements}/ci-requirements.in | 0 .../requirements}/ci-requirements.txt | 178 +++++++++--------- .../requirements}/dev-requirements.in | 0 .../requirements}/dev-requirements.txt | 68 ++++--- .../requirements}/requirements.in | 0 .../requirements}/requirements.txt | 70 ++++--- 11 files changed, 162 insertions(+), 164 deletions(-) rename {requirements => code/requirements}/ci-requirements.in (100%) rename {requirements => code/requirements}/ci-requirements.txt (71%) rename {requirements => code/requirements}/dev-requirements.in (100%) rename {requirements => code/requirements}/dev-requirements.txt (95%) rename {requirements => code/requirements}/requirements.in (100%) rename {requirements => code/requirements}/requirements.txt (92%) diff --git a/.github/workflows/memote-history.yml b/.github/workflows/memote-history.yml index 331b4650..59baf6bb 100644 --- a/.github/workflows/memote-history.yml +++ b/.github/workflows/memote-history.yml @@ -18,7 +18,7 @@ jobs: python-version: '3.9.7' - name: Install memote - run: pip install -r requirements/ci-requirements.txt + run: pip install -r code/requirements/ci-requirements.txt - name: Setup variables id: setup diff --git a/.github/workflows/memote-run.yml b/.github/workflows/memote-run.yml index fde84724..f75354e9 100644 --- a/.github/workflows/memote-run.yml +++ b/.github/workflows/memote-run.yml @@ -16,7 +16,7 @@ jobs: python-version: '3.9.7' - name: Install memote - run: pip install -r requirements/ci-requirements.txt + run: pip install -r code/requirements/ci-requirements.txt - name: Convert model run: | diff --git a/.github/workflows/memote_release.yml b/.github/workflows/memote_release.yml index f793f806..2af1eae9 100644 --- a/.github/workflows/memote_release.yml +++ b/.github/workflows/memote_release.yml @@ -26,7 +26,7 @@ jobs: python-version: '3.9.7' - name: Install memote - run: pip install -r requirements/requirements.txt + run: pip install -r code/requirements/requirements.txt - name: Memote run run: | diff --git a/.github/workflows/yaml-validation.yml b/.github/workflows/yaml-validation.yml index 43bc4d1c..8e74367d 100644 --- a/.github/workflows/yaml-validation.yml +++ b/.github/workflows/yaml-validation.yml @@ -35,5 +35,5 @@ jobs: - name: Import with cobrapy run: | - pip install -r requirements/ci-requirements.txt + pip install -r code/requirements/ci-requirements.txt python -c "import cobra ; cobra.io.load_yaml_model('model/yeast-GEM.yml')" diff --git a/README.md b/README.md index 3a707ac6..6acb1d3f 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ Please see the installation instructions for each software package. If you want to use any of the [provided](https://github.com/SysBioChalmers/yeast-GEM/tree/main/code) Python functions, you may create an environment with all requirements: ```bash - pip install -r requirements/requirements.txt # installs all dependencies + pip install -r code/requirements/requirements.txt # installs all dependencies touch .env # creates a .env file for locating the root ``` diff --git a/requirements/ci-requirements.in b/code/requirements/ci-requirements.in similarity index 100% rename from requirements/ci-requirements.in rename to code/requirements/ci-requirements.in diff --git a/requirements/ci-requirements.txt b/code/requirements/ci-requirements.txt similarity index 71% rename from requirements/ci-requirements.txt rename to code/requirements/ci-requirements.txt index e988b7cc..7ac4b8cd 100644 --- a/requirements/ci-requirements.txt +++ b/code/requirements/ci-requirements.txt @@ -1,44 +1,49 @@ # -# This file is autogenerated by pip-compile +# This file is autogenerated by pip-compile with python 3.9 # To update, run: # # pip-compile ci-requirements.in # alabaster==0.7.12 # via sphinx +anyio==3.6.1 + # via httpcore appdirs==1.4.4 # via cobra -arrow==1.0.3 +arrow==1.2.2 # via jinja2-time -attrs==20.3.0 +attrs==21.4.0 # via + # jsonlines # jsonschema # pytest -babel==2.9.1 +babel==2.10.3 # via sphinx binaryornot==0.4.4 # via cookiecutter -boto3==1.17.49 +boto3==1.24.10 # via tabulator -botocore==1.20.49 +botocore==1.27.10 # via # boto3 # s3transfer cached-property==1.5.2 # via tableschema -certifi==2020.12.5 +certifi==2022.6.15 # via + # httpcore # httpx # requests -cffi==1.14.5 +cffi==1.15.0 # via cryptography chardet==4.0.0 # via # binaryornot # datapackage - # requests # tabulator -click==7.1.2 +charset-normalizer==2.0.12 + # via requests +click==8.1.3 # via # click-configfile # click-default-group @@ -54,21 +59,19 @@ click-configfile==0.2.3 # via memote click-default-group==1.2.2 # via goodtables -click-log==0.3.2 +click-log==0.4.0 # via memote -cobra==0.22.1 +cobra==0.25.0 # via # -r ci-requirements.in # memote -colorama==0.4.4 - # via rich commonmark==0.9.1 # via rich -configparser==5.0.2 +configparser==5.2.0 # via click-configfile -cookiecutter==1.7.2 +cookiecutter==2.1.1 # via memote -cryptography==3.4.7 +cryptography==37.0.2 # via travis-encrypt datapackage==1.15.2 # via goodtables @@ -76,49 +79,52 @@ depinfo==1.7.0 # via # cobra # memote -diskcache==5.2.1 +diskcache==5.4.0 # via cobra -docutils==0.17 +docutils==0.18.1 # via # sphinx # statistics -et-xmlfile==1.0.1 +et-xmlfile==1.1.0 # via openpyxl future==0.18.2 # via # cobra # memote -gitdb==4.0.7 +gitdb==4.0.9 # via gitpython -gitpython==3.1.14 +gitpython==3.1.27 # via memote goodtables==2.5.4 # via memote -greenlet==1.0.0 +greenlet==1.1.2 # via sqlalchemy h11==0.12.0 # via httpcore -httpcore==0.12.3 +httpcore==0.15.0 # via httpx -httpx==0.17.1 +httpx==0.23.0 # via cobra -idna==2.10 +idna==3.3 # via + # anyio # requests # rfc3986 ijson==3.1.4 # via tabulator -imagesize==1.2.0 +imagesize==1.3.0 # via sphinx -importlib-resources==5.1.2 +importlib-metadata==4.11.4 + # via sphinx +importlib-resources==5.8.0 # via # cobra # memote iniconfig==1.1.1 # via pytest -isodate==0.6.0 +isodate==0.6.1 # via tableschema -jinja2==2.11.3 +jinja2==3.1.2 # via # cookiecutter # jinja2-time @@ -127,89 +133,87 @@ jinja2==2.11.3 # sphinx jinja2-time==0.2.0 # via cookiecutter -jmespath==0.10.0 +jmespath==1.0.0 # via # boto3 # botocore -jsonlines==2.0.0 +jsonlines==3.0.0 # via tabulator -jsonpointer==2.1 +jsonpointer==2.3 # via datapackage -jsonschema==3.2.0 +jsonschema==4.6.0 # via # datapackage # tableschema linear-tsv==1.1.0 # via tabulator -markupsafe==1.1.1 - # via - # cookiecutter - # jinja2 +markupsafe==2.1.1 + # via jinja2 memote==0.13.0 # via -r ci-requirements.in mpmath==1.2.1 # via sympy -numpy==1.20.2 +numpy==1.22.4 # via # cobra # pandas -numpydoc==1.1.0 +numpydoc==1.4.0 # via memote -openpyxl==3.0.7 +openpyxl==3.0.10 # via tabulator optlang==1.5.2 # via cobra -packaging==20.9 +packaging==21.3 # via # pytest # sphinx -pandas==1.2.3 +pandas==1.4.2 # via # cobra # memote -pluggy==0.13.1 +pluggy==1.0.0 # via pytest -poyo==0.5.0 - # via cookiecutter -py==1.10.0 +py==1.11.0 # via pytest -pycparser==2.20 +pycparser==2.21 # via cffi -pydantic==1.8.2 +pydantic==1.9.1 # via cobra -pygments==2.8.1 +pygments==2.12.0 # via # rich # sphinx -pylru==1.2.0 +pylru==1.2.1 # via memote -pyparsing==2.4.7 +pyparsing==3.0.9 # via packaging pyperclip==1.6.0 # via travis-encrypt -pyrsistent==0.17.3 +pyrsistent==0.18.1 # via jsonschema -pytest==6.2.3 +pytest==7.1.2 # via memote -python-dateutil==2.8.1 +python-dateutil==2.8.2 # via # arrow # botocore # pandas # tableschema -python-dotenv==0.19.0 +python-dotenv==0.20.0 # via -r ci-requirements.in -python-libsbml==5.19.0 +python-libsbml==5.19.5 # via cobra -python-slugify==4.0.1 +python-slugify==6.1.2 # via cookiecutter -pytz==2021.1 +pytz==2022.1 # via # babel # pandas -pyyaml==5.4.1 - # via travis-encrypt -requests==2.25.1 +pyyaml==6.0 + # via + # cookiecutter + # travis-encrypt +requests==2.28.0 # via # cookiecutter # datapackage @@ -219,71 +223,70 @@ requests==2.25.1 # tableschema # tabulator # travis-encrypt -rfc3986[idna2008]==1.4.0 +rfc3986[idna2008]==1.5.0 # via # httpx # tableschema -rich==10.7.0 +rich==12.4.4 # via cobra -ruamel.yaml==0.17.4 +ruamel-yaml==0.17.21 # via # cobra # memote -ruamel.yaml.clib==0.2.2 - # via ruamel.yaml -s3transfer==0.3.6 +ruamel-yaml-clib==0.2.6 + # via ruamel-yaml +s3transfer==0.6.0 # via boto3 -simpleeval==0.9.10 +simpleeval==0.9.12 # via goodtables -six==1.15.0 +six==1.16.0 # via # click-configfile - # cookiecutter # datapackage # goodtables # isodate - # jsonschema # linear-tsv # memote # optlang # python-dateutil # tableschema # tabulator -smmap==4.0.0 +smmap==5.0.0 # via gitdb sniffio==1.2.0 # via + # anyio # httpcore # httpx -snowballstemmer==2.1.0 +snowballstemmer==2.2.0 # via sphinx -sphinx==3.5.3 +sphinx==5.0.1 # via numpydoc sphinxcontrib-applehelp==1.0.2 # via sphinx sphinxcontrib-devhelp==1.0.2 # via sphinx -sphinxcontrib-htmlhelp==1.0.3 +sphinxcontrib-htmlhelp==2.0.0 # via sphinx sphinxcontrib-jsmath==1.0.1 # via sphinx sphinxcontrib-qthelp==1.0.3 # via sphinx -sphinxcontrib-serializinghtml==1.1.4 +sphinxcontrib-serializinghtml==1.1.5 # via sphinx -sqlalchemy==1.4.7 +sqlalchemy==1.4.37 # via # memote # tabulator statistics==1.0.3.5 # via goodtables -swiglpk==5.0.3 +swiglpk==5.0.5 # via # cobra # optlang -symengine==0.8.1 +symengine==0.9.2 # via -r ci-requirements.in -sympy==1.8 +sympy==1.10.1 # via # memote # optlang @@ -298,23 +301,24 @@ tabulator==1.53.5 # tableschema text-unidecode==1.3 # via python-slugify -toml==0.10.2 +tomli==2.0.1 # via pytest travis-encrypt==1.1.2 # via memote -typing-extensions==3.7.4.3 +typing-extensions==4.2.0 # via pydantic unicodecsv==0.14.1 # via # datapackage # tableschema # tabulator -urllib3==1.26.5 +urllib3==1.26.9 # via # botocore # requests xlrd==2.0.1 # via tabulator - -# The following packages are considered to be unsafe in a requirements file: -# setuptools +zipp==3.8.0 + # via + # importlib-metadata + # importlib-resources diff --git a/requirements/dev-requirements.in b/code/requirements/dev-requirements.in similarity index 100% rename from requirements/dev-requirements.in rename to code/requirements/dev-requirements.in diff --git a/requirements/dev-requirements.txt b/code/requirements/dev-requirements.txt similarity index 95% rename from requirements/dev-requirements.txt rename to code/requirements/dev-requirements.txt index eeb2a265..556d04cf 100644 --- a/requirements/dev-requirements.txt +++ b/code/requirements/dev-requirements.txt @@ -38,7 +38,7 @@ attrs==21.4.0 # jsonlines # jsonschema # pytest -babel==2.10.1 +babel==2.10.3 # via # -r requirements.txt # sphinx @@ -58,11 +58,11 @@ bleach==5.0.0 # via # -r requirements.txt # nbconvert -boto3==1.23.2 +boto3==1.24.10 # via # -r requirements.txt # tabulator -botocore==1.26.2 +botocore==1.27.10 # via # -r requirements.txt # boto3 @@ -71,7 +71,7 @@ cached-property==1.5.2 # via # -r requirements.txt # tableschema -certifi==2021.10.8 +certifi==2022.6.15 # via # -r requirements.txt # httpcore @@ -91,7 +91,6 @@ chardet==4.0.0 charset-normalizer==2.0.12 # via # -r requirements.txt - # httpx # requests click==8.1.3 # via @@ -131,7 +130,7 @@ configparser==5.2.0 # via # -r requirements.txt # click-configfile -cookiecutter==1.7.3 +cookiecutter==2.1.1 # via # -r requirements.txt # memote @@ -164,7 +163,7 @@ diskcache==5.4.0 # via # -r requirements.txt # cobra -docutils==0.17.1 +docutils==0.18.1 # via # -r requirements.txt # sphinx @@ -211,11 +210,11 @@ h11==0.12.0 # via # -r requirements.txt # httpcore -httpcore==0.14.7 +httpcore==0.15.0 # via # -r requirements.txt # httpx -httpx==0.22.0 +httpx==0.23.0 # via # -r requirements.txt # cobra @@ -233,11 +232,11 @@ imagesize==1.3.0 # via # -r requirements.txt # sphinx -importlib-metadata==4.11.3 +importlib-metadata==4.11.4 # via # -r requirements.txt # sphinx -importlib-resources==5.7.1 +importlib-resources==5.8.0 # via # -r requirements.txt # cobra @@ -246,11 +245,11 @@ iniconfig==1.1.1 # via # -r requirements.txt # pytest -ipykernel==6.13.0 +ipykernel==6.15.0 # via # -r requirements.txt # notebook -ipython==8.3.0 +ipython==8.4.0 # via # -r requirements.txt # ipykernel @@ -293,13 +292,13 @@ jsonpointer==2.3 # via # -r requirements.txt # datapackage -jsonschema==4.5.1 +jsonschema==4.6.0 # via # -r requirements.txt # datapackage # nbformat # tableschema -jupyter-client==7.3.1 +jupyter-client==7.3.4 # via # -r requirements.txt # ipykernel @@ -340,7 +339,7 @@ mpmath==1.2.1 # via # -r requirements.txt # sympy -nbclient==0.6.3 +nbclient==0.6.4 # via # -r requirements.txt # nbconvert @@ -361,18 +360,18 @@ nest-asyncio==1.5.5 # jupyter-client # nbclient # notebook -notebook==6.4.11 +notebook==6.4.12 # via -r requirements.txt -numpy==1.22.3 +numpy==1.22.4 # via # -r requirements.txt # cobra # pandas -numpydoc==1.3.1 +numpydoc==1.4.0 # via # -r requirements.txt # memote -openpyxl==3.0.9 +openpyxl==3.0.10 # via # -r requirements.txt # tabulator @@ -410,16 +409,12 @@ pickleshare==0.7.5 # via # -r requirements.txt # ipython -pip-tools==6.6.1 +pip-tools==6.6.2 # via -r dev-requirements.in pluggy==1.0.0 # via # -r requirements.txt # pytest -poyo==0.5.0 - # via - # -r requirements.txt - # cookiecutter prometheus-client==0.14.1 # via # -r requirements.txt @@ -428,7 +423,7 @@ prompt-toolkit==3.0.29 # via # -r requirements.txt # ipython -psutil==5.9.0 +psutil==5.9.1 # via # -r requirements.txt # ipykernel @@ -449,7 +444,7 @@ pycparser==2.21 # via # -r requirements.txt # cffi -pydantic==1.9.0 +pydantic==1.9.1 # via # -r requirements.txt # cobra @@ -506,13 +501,15 @@ pytz==2022.1 pyyaml==6.0 # via # -r requirements.txt + # cookiecutter # travis-encrypt -pyzmq==22.3.0 +pyzmq==23.1.0 # via # -r requirements.txt + # ipykernel # jupyter-client # notebook -requests==2.27.1 +requests==2.28.0 # via # -r requirements.txt # cookiecutter @@ -528,7 +525,7 @@ rfc3986[idna2008]==1.5.0 # -r requirements.txt # httpx # tableschema -rich==12.4.1 +rich==12.4.4 # via # -r requirements.txt # cobra @@ -541,7 +538,7 @@ ruamel-yaml-clib==0.2.6 # via # -r requirements.txt # ruamel-yaml -s3transfer==0.5.2 +s3transfer==0.6.0 # via # -r requirements.txt # boto3 @@ -559,7 +556,6 @@ six==1.16.0 # asttokens # bleach # click-configfile - # cookiecutter # datapackage # goodtables # isodate @@ -587,7 +583,7 @@ soupsieve==2.3.2.post1 # via # -r requirements.txt # beautifulsoup4 -sphinx==4.5.0 +sphinx==5.0.1 # via # -r requirements.txt # numpydoc @@ -615,12 +611,12 @@ sphinxcontrib-serializinghtml==1.1.5 # via # -r requirements.txt # sphinx -sqlalchemy==1.4.36 +sqlalchemy==1.4.37 # via # -r requirements.txt # memote # tabulator -stack-data==0.2.0 +stack-data==0.3.0 # via # -r requirements.txt # ipython @@ -675,7 +671,7 @@ tornado==6.1 # jupyter-client # notebook # terminado -traitlets==5.2.1.post0 +traitlets==5.3.0 # via # -r requirements.txt # ipykernel diff --git a/requirements/requirements.in b/code/requirements/requirements.in similarity index 100% rename from requirements/requirements.in rename to code/requirements/requirements.in diff --git a/requirements/requirements.txt b/code/requirements/requirements.txt similarity index 92% rename from requirements/requirements.txt rename to code/requirements/requirements.txt index c1352e03..acb3519a 100644 --- a/requirements/requirements.txt +++ b/code/requirements/requirements.txt @@ -23,7 +23,7 @@ attrs==21.4.0 # jsonlines # jsonschema # pytest -babel==2.10.1 +babel==2.10.3 # via sphinx backcall==0.2.0 # via ipython @@ -33,15 +33,15 @@ binaryornot==0.4.4 # via cookiecutter bleach==5.0.0 # via nbconvert -boto3==1.23.2 +boto3==1.24.10 # via tabulator -botocore==1.26.2 +botocore==1.27.10 # via # boto3 # s3transfer cached-property==1.5.2 # via tableschema -certifi==2021.10.8 +certifi==2022.6.15 # via # httpcore # httpx @@ -56,9 +56,7 @@ chardet==4.0.0 # datapackage # tabulator charset-normalizer==2.0.12 - # via - # httpx - # requests + # via requests click==8.1.3 # via # click-configfile @@ -85,7 +83,7 @@ commonmark==0.9.1 # via rich configparser==5.2.0 # via click-configfile -cookiecutter==1.7.3 +cookiecutter==2.1.1 # via memote cryptography==37.0.2 # via travis-encrypt @@ -103,7 +101,7 @@ depinfo==1.7.0 # memote diskcache==5.4.0 # via cobra -docutils==0.17.1 +docutils==0.18.1 # via # sphinx # statistics @@ -131,9 +129,9 @@ greenlet==1.1.2 # via sqlalchemy h11==0.12.0 # via httpcore -httpcore==0.14.7 +httpcore==0.15.0 # via httpx -httpx==0.22.0 +httpx==0.23.0 # via cobra idna==3.3 # via @@ -144,17 +142,17 @@ ijson==3.1.4 # via tabulator imagesize==1.3.0 # via sphinx -importlib-metadata==4.11.3 +importlib-metadata==4.11.4 # via sphinx -importlib-resources==5.7.1 +importlib-resources==5.8.0 # via # cobra # memote iniconfig==1.1.1 # via pytest -ipykernel==6.13.0 +ipykernel==6.15.0 # via notebook -ipython==8.3.0 +ipython==8.4.0 # via ipykernel ipython-genutils==0.2.0 # via notebook @@ -181,12 +179,12 @@ jsonlines==3.0.0 # via tabulator jsonpointer==2.3 # via datapackage -jsonschema==4.5.1 +jsonschema==4.6.0 # via # datapackage # nbformat # tableschema -jupyter-client==7.3.1 +jupyter-client==7.3.4 # via # ipykernel # nbclient @@ -215,7 +213,7 @@ mistune==0.8.4 # via nbconvert mpmath==1.2.1 # via sympy -nbclient==0.6.3 +nbclient==0.6.4 # via nbconvert nbconvert==6.5.0 # via notebook @@ -230,15 +228,15 @@ nest-asyncio==1.5.5 # jupyter-client # nbclient # notebook -notebook==6.4.11 +notebook==6.4.12 # via -r requirements.in -numpy==1.22.3 +numpy==1.22.4 # via # cobra # pandas -numpydoc==1.3.1 +numpydoc==1.4.0 # via memote -openpyxl==3.0.9 +openpyxl==3.0.10 # via tabulator optlang==1.5.2 # via cobra @@ -262,13 +260,11 @@ pickleshare==0.7.5 # via ipython pluggy==1.0.0 # via pytest -poyo==0.5.0 - # via cookiecutter prometheus-client==0.14.1 # via notebook prompt-toolkit==3.0.29 # via ipython -psutil==5.9.0 +psutil==5.9.1 # via ipykernel ptyprocess==0.7.0 # via @@ -280,7 +276,7 @@ py==1.11.0 # via pytest pycparser==2.21 # via cffi -pydantic==1.9.0 +pydantic==1.9.1 # via cobra pygments==2.12.0 # via @@ -316,12 +312,15 @@ pytz==2022.1 # babel # pandas pyyaml==6.0 - # via travis-encrypt -pyzmq==22.3.0 # via + # cookiecutter + # travis-encrypt +pyzmq==23.1.0 + # via + # ipykernel # jupyter-client # notebook -requests==2.27.1 +requests==2.28.0 # via # cookiecutter # datapackage @@ -335,7 +334,7 @@ rfc3986[idna2008]==1.5.0 # via # httpx # tableschema -rich==12.4.1 +rich==12.4.4 # via cobra ruamel-yaml==0.17.21 # via @@ -343,7 +342,7 @@ ruamel-yaml==0.17.21 # memote ruamel-yaml-clib==0.2.6 # via ruamel-yaml -s3transfer==0.5.2 +s3transfer==0.6.0 # via boto3 send2trash==1.8.0 # via notebook @@ -354,7 +353,6 @@ six==1.16.0 # asttokens # bleach # click-configfile - # cookiecutter # datapackage # goodtables # isodate @@ -375,7 +373,7 @@ snowballstemmer==2.2.0 # via sphinx soupsieve==2.3.2.post1 # via beautifulsoup4 -sphinx==4.5.0 +sphinx==5.0.1 # via numpydoc sphinxcontrib-applehelp==1.0.2 # via sphinx @@ -389,11 +387,11 @@ sphinxcontrib-qthelp==1.0.3 # via sphinx sphinxcontrib-serializinghtml==1.1.5 # via sphinx -sqlalchemy==1.4.36 +sqlalchemy==1.4.37 # via # memote # tabulator -stack-data==0.2.0 +stack-data==0.3.0 # via ipython statistics==1.0.3.5 # via goodtables @@ -430,7 +428,7 @@ tornado==6.1 # jupyter-client # notebook # terminado -traitlets==5.2.1.post0 +traitlets==5.3.0 # via # ipykernel # ipython