From 4e93ff781a7c03f8314edec6c7de54f73b537cf8 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Tue, 29 Aug 2023 17:21:51 +0200 Subject: [PATCH 01/28] Set maximum ms2deepscore version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 7865cffa..87cfb92e 100644 --- a/setup.py +++ b/setup.py @@ -37,7 +37,7 @@ "tensorflow-metal==0.5.0;platform_machine=='arm64'", "tensorflow<2.9;platform_machine!='arm64'", #tensorflow <2.9 for change in error bar plotting "scikit-learn", - "ms2deepscore", + "ms2deepscore<=0.4.0", "gensim>=4.0.0", "pandas>=1.2.5,<2.0.0", "matchmsextras==0.4.0", From 4f31b577d90a884f0c4b7aed6d1bcb33ad8a0263 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Tue, 29 Aug 2023 17:42:02 +0200 Subject: [PATCH 02/28] Update to yml to new setup.py --- environment.yml | 345 ++++++++++++++++++++---------------------------- 1 file changed, 145 insertions(+), 200 deletions(-) diff --git a/environment.yml b/environment.yml index f2d0d2e0..f70e018a 100644 --- a/environment.yml +++ b/environment.yml @@ -6,220 +6,165 @@ channels: dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=2_gnu - - abseil-cpp=20210324.2=h9c3ff4c_0 - - absl-py=1.4.0=pyhd8ed1ab_0 - - aiohttp=3.8.5=py38h01eb140_0 - - aiosignal=1.3.1=pyhd8ed1ab_0 - - astunparse=1.6.3=pyhd8ed1ab_0 - - async-timeout=4.0.3=pyhd8ed1ab_0 - - attrs=23.1.0=pyh71513ae_1 - - blinker=1.6.2=pyhd8ed1ab_0 - - boost=1.78.0=py38h4e30db6_4 - - boost-cpp=1.78.0=h5adbc97_2 - - brotli=1.0.9=h166bdaf_9 - - brotli-bin=1.0.9=h166bdaf_9 - - brotli-python=1.0.9=py38hfa26641_9 - bzip2=1.0.8=h7f98852_4 - - c-ares=1.19.1=hd590300_0 - ca-certificates=2023.7.22=hbcca054_0 - - cached-property=1.5.2=hd8ed1ab_1 - - cached_property=1.5.2=pyha770c72_1 - - cachetools=5.3.1=pyhd8ed1ab_0 - - cairo=1.16.0=ha61ee94_1014 - - certifi=2023.7.22=pyhd8ed1ab_0 - - cffi=1.15.1=py38h4a40e3a_3 - - charset-normalizer=3.2.0=pyhd8ed1ab_0 - - click=8.1.7=unix_pyh707e725_0 - - colorama=0.4.6=pyhd8ed1ab_0 - - coloredlogs=15.0.1=pyhd8ed1ab_3 - - contourpy=1.1.0=py38h7f3f72f_0 - - cryptography=39.0.0=py38h1724139_0 - - cycler=0.11.0=pyhd8ed1ab_0 - - deprecated=1.2.14=pyh1a96a4e_0 - - expat=2.5.0=hcb278e6_1 - - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 - - font-ttf-inconsolata=3.000=h77eed37_0 - - font-ttf-source-code-pro=2.038=h77eed37_0 - - font-ttf-ubuntu=0.83=hab24e00_0 - - fontconfig=2.14.2=h14ed4e7_0 - - fonts-conda-ecosystem=1=0 - - fonts-conda-forge=1=0 - - fonttools=4.42.1=py38h01eb140_0 - - freetype=2.12.1=hca18f0e_1 - - freetype-py=2.3.0=pyhd8ed1ab_0 - - frozenlist=1.4.0=py38h01eb140_0 - - fst-pso=1.8.1=pyhd8ed1ab_0 - - fuzzytm=2.0.5=pyhd8ed1ab_0 - - gast=0.5.4=pyhd8ed1ab_0 - - gensim=4.3.2=py38h53bb729_0 - - gettext=0.21.1=h27087fc_0 - - giflib=5.2.1=h0b41bf4_3 - - gmp=6.2.1=h58526e2_0 - - gmpy2=2.1.2=py38h793c122_1 - - google-auth=2.17.3=pyh1a96a4e_0 - - google-auth-oauthlib=0.4.6=pyhd8ed1ab_0 - - google-pasta=0.2.0=pyh8c360ce_0 - - greenlet=2.0.2=py38h17151c0_1 - - grpc-cpp=1.45.2=h9d3bbbb_5 - - grpcio=1.45.0=py38ha0cdfde_0 - - h5py=3.9.0=nompi_py38h89e2d6c_100 - - hdf5=1.14.0=nompi_h5231ba7_103 - - humanfriendly=10.0=py38h578d9bd_4 - - icu=70.1=h27087fc_0 - - idna=3.4=pyhd8ed1ab_0 - - importlib-metadata=6.8.0=pyha770c72_0 - - importlib-resources=6.0.1=pyhd8ed1ab_0 - - importlib_resources=6.0.1=pyhd8ed1ab_0 - - joblib=1.3.2=pyhd8ed1ab_0 - - jpeg=9e=h0b41bf4_3 - - keras=2.8.0=pyhd8ed1ab_0 - - keras-preprocessing=1.1.2=pyhd8ed1ab_0 - - keyutils=1.6.1=h166bdaf_0 - - kiwisolver=1.4.5=py38h7f3f72f_0 - - krb5=1.20.1=hf9c8cef_0 - - lcms2=2.15=hfd0df8a_0 - ld_impl_linux-64=2.40=h41732ed_0 - - lerc=4.0.0=h27087fc_0 - - libaec=1.0.6=hcb278e6_1 - - libblas=3.9.0=17_linux64_openblas - - libbrotlicommon=1.0.9=h166bdaf_9 - - libbrotlidec=1.0.9=h166bdaf_9 - - libbrotlienc=1.0.9=h166bdaf_9 - - libcblas=3.9.0=17_linux64_openblas - - libcurl=7.87.0=h6312ad2_0 - - libdeflate=1.17=h0b41bf4_0 - - libedit=3.1.20191231=he28a2e2_2 - - libev=4.33=h516909a_1 - - libexpat=2.5.0=hcb278e6_1 - libffi=3.4.2=h7f98852_5 - libgcc-ng=13.1.0=he5830b7_0 - - libgfortran-ng=13.1.0=h69a702a_0 - - libgfortran5=13.1.0=h15d22d2_0 - - libglib=2.76.4=hebfc3b9_0 - libgomp=13.1.0=he5830b7_0 - - libiconv=1.17=h166bdaf_0 - - liblapack=3.9.0=17_linux64_openblas - - libllvm14=14.0.6=hcd5def8_4 - - libnghttp2=1.51.0=hdcd2b5c_0 - libnsl=2.0.0=h7f98852_0 - - libopenblas=0.3.23=pthreads_h80387f5_0 - - libpng=1.6.39=h753d276_0 - - libprotobuf=3.20.3=h3eb15da_0 - libsqlite=3.43.0=h2797004_0 - - libssh2=1.10.0=haa6b8db_3 - - libstdcxx-ng=13.1.0=hfd8a6a1_0 - - libtiff=4.5.0=h6adf6a1_2 - libuuid=2.38.1=h0b41bf4_0 - - libwebp-base=1.3.1=hd590300_0 - - libxcb=1.13=h7f98852_1004 - - libxml2=2.10.3=hca2bb57_4 - - libxslt=1.1.37=h873f0b0_0 - libzlib=1.2.13=hd590300_5 - - llvmlite=0.40.1=py38h94a1851_0 - - lxml=4.9.2=py38h215a2d7_0 - - markdown=3.4.4=pyhd8ed1ab_0 - - markupsafe=2.1.3=py38h01eb140_0 - - matchms=0.17.0=pyh7cba7a3_0 - - matchmsextras=0.4.1=pyhdfd78af_0 - - matplotlib-base=3.7.2=py38hf5b0b65_0 - - miniful=0.0.6=pyhd8ed1ab_0 - - mpc=1.3.1=hfe3b2da_0 - - mpfr=4.2.0=hb012696_0 - - mpmath=1.3.0=pyhd8ed1ab_0 - - ms2deepscore=0.5.0=pyhdfd78af_0 - - ms2query=1.2.2=pyhdfd78af_0 - - multidict=6.0.4=py38h1de0b5d_0 - - munkres=1.1.4=pyh9f0ad1d_0 - ncurses=6.4=hcb278e6_0 - - networkx=3.1=pyhd8ed1ab_0 - - numba=0.57.1=py38hd559b08_0 - - numpy=1.24.4=py38h59b608b_0 - - oauthlib=3.2.2=pyhd8ed1ab_0 - - onnx=1.12.0=py38h8d49f1e_0 - - onnxconverter-common=1.13.0=pyhd8ed1ab_0 - - onnxruntime=1.15.1=py38h896e202_2_cpu - - openjpeg=2.5.0=hfec8fc6_2 - - openssl=1.1.1v=hd590300_0 - - opt_einsum=3.3.0=pyhd8ed1ab_1 - - packaging=23.1=pyhd8ed1ab_0 - - pandas=1.5.3=py38hdc8b05c_1 - - pcre2=10.40=hc3806b6_0 - - pickydict=0.4.0=pyhd8ed1ab_0 - - pillow=9.4.0=py38hde6dc18_1 + - openssl=3.1.2=hd590300_0 - pip=23.2.1=pyhd8ed1ab_0 - - pixman=0.40.0=h36c2ea0_0 - - platformdirs=3.10.0=pyhd8ed1ab_0 - - pooch=1.7.0=pyha770c72_3 - - protobuf=3.20.3=py38h8dc9893_1 - - pthread-stubs=0.4=h36c2ea0_1001 - - pubchempy=1.0.4=py_0 - - pyasn1=0.4.8=py_0 - - pyasn1-modules=0.2.7=py_0 - - pycairo=1.24.0=py38h1a1917b_0 - - pycparser=2.21=pyhd8ed1ab_0 - - pyfume=0.2.25=pyhd8ed1ab_0 - - pyjwt=2.8.0=pyhd8ed1ab_0 - - pyopenssl=23.2.0=pyhd8ed1ab_1 - - pyparsing=3.0.9=pyhd8ed1ab_0 - - pysocks=1.7.1=pyha2e5f31_6 - - pyteomics=4.6=pyh7cba7a3_0 - - python=3.8.15=h257c98d_0_cpython - - python-dateutil=2.8.2=pyhd8ed1ab_0 - - python-flatbuffers=23.5.26=pyhd8ed1ab_0 - - python-louvain=0.16=pyhd8ed1ab_0 - - python_abi=3.8=3_cp38 - - pytz=2023.3=pyhd8ed1ab_0 - - pyu2f=0.1.5=pyhd8ed1ab_0 - - rdkit=2023.03.3=py38h36d2b2f_0 - - re2=2022.06.01=h27087fc_1 + - python=3.8.17=he550d4f_0_cpython - readline=8.2=h8228510_1 - - reportlab=4.0.4=py38h01eb140_0 - - requests=2.31.0=pyhd8ed1ab_0 - - requests-oauthlib=1.3.1=pyhd8ed1ab_0 - - rlpycairo=0.2.0=pyhd8ed1ab_0 - - rsa=4.9=pyhd8ed1ab_0 - - scikit-learn=1.3.0=py38hc099248_0 - - scipy=1.10.1=py38h59b608b_3 - setuptools=68.1.2=pyhd8ed1ab_0 - - simpful=2.11.0=pyhd8ed1ab_0 - - six=1.16.0=pyh6c4a22f_0 - - skl2onnx=1.15.0=pyhd8ed1ab_0 - - smart_open=6.3.0=pyhd8ed1ab_1 - - snappy=1.1.10=h9fff704_0 - - spec2vec=0.8.0=pyhdfd78af_0 - - sqlalchemy=2.0.20=py38h01eb140_0 - - sqlite=3.43.0=h2c6b66d_0 - - sympy=1.12=pypyh9d50eac_103 - - tensorboard=2.8.0=pyhd8ed1ab_1 - - tensorboard-data-server=0.6.1=py38h2b5fc30_4 - - tensorboard-plugin-wit=1.8.1=pyhd8ed1ab_0 - - tensorflow=2.8.1=cpu_py38h66f0ec1_0 - - tensorflow-base=2.8.1=cpu_py38hc7a75a0_0 - - tensorflow-estimator=2.8.1=cpu_py38h4e23bc6_0 - - termcolor=2.3.0=pyhd8ed1ab_0 - - threadpoolctl=3.2.0=pyha21a80b_0 - tk=8.6.12=h27826a3_0 - - tqdm=4.66.1=pyhd8ed1ab_0 - - typing-extensions=4.7.1=hd8ed1ab_0 - - typing_extensions=4.7.1=pyha770c72_0 - - unicodedata2=15.0.0=py38h0a891b7_0 - - urllib3=2.0.4=pyhd8ed1ab_0 - - werkzeug=2.3.7=pyhd8ed1ab_0 - wheel=0.41.2=pyhd8ed1ab_0 - - wrapt=1.15.0=py38h1de0b5d_0 - - xorg-kbproto=1.0.7=h7f98852_1002 - - xorg-libice=1.1.1=hd590300_0 - - xorg-libsm=1.2.4=h7391055_0 - - xorg-libx11=1.8.4=h0b41bf4_0 - - xorg-libxau=1.0.11=hd590300_0 - - xorg-libxdmcp=1.1.3=h7f98852_0 - - xorg-libxext=1.3.4=h0b41bf4_2 - - xorg-libxrender=0.9.10=h7f98852_1003 - - xorg-renderproto=0.11.1=h7f98852_1002 - - xorg-xextproto=7.3.0=h0b41bf4_1003 - - xorg-xproto=7.0.31=h7f98852_1007 - xz=5.2.6=h166bdaf_0 - - yarl=1.9.2=py38h01eb140_0 - - zipp=3.16.2=pyhd8ed1ab_0 - - zlib=1.2.13=hd590300_5 - - zstd=1.5.2=hfc55251_7 + - pip: + - absl-py==1.4.0 + - alabaster==0.7.13 + - astroid==2.15.6 + - astunparse==1.6.3 + - babel==2.12.1 + - build==0.10.0 + - bump2version==1.0.1 + - cachetools==5.3.1 + - certifi==2023.7.22 + - charset-normalizer==3.2.0 + - coloredlogs==15.0.1 + - contourpy==1.1.0 + - coverage==7.3.0 + - cycler==0.11.0 + - deprecated==1.2.14 + - dill==0.3.7 + - docutils==0.16 + - dodgy==0.2.1 + - exceptiongroup==1.1.3 + - flake8==5.0.4 + - flake8-polyfill==1.0.2 + - flatbuffers==23.5.26 + - fonttools==4.42.1 + - gast==0.5.4 + - gensim==4.3.2 + - gitdb==4.0.10 + - gitpython==3.1.32 + - google-auth==2.22.0 + - google-auth-oauthlib==0.4.6 + - google-pasta==0.2.0 + - grpcio==1.57.0 + - h5py==3.9.0 + - humanfriendly==10.0 + - idna==3.4 + - imagesize==1.4.1 + - importlib-metadata==6.8.0 + - importlib-resources==6.0.1 + - iniconfig==2.0.0 + - isort==5.12.0 + - jinja2==3.1.2 + - joblib==1.3.2 + - keras==2.8.0 + - keras-preprocessing==1.1.2 + - kiwisolver==1.4.5 + - lazy-object-proxy==1.9.0 + - libclang==16.0.6 + - llvmlite==0.40.1 + - lxml==4.9.3 + - markdown==3.4.4 + - markupsafe==2.1.3 + - matchms==0.17.0 + - matchmsextras==0.4.0 + - matplotlib==3.7.2 + - mccabe==0.7.0 + - mpmath==1.3.0 + - ms2deepscore==0.4.0 + - ms2query==1.2.2 + - networkx==3.1 + - numba==0.57.1 + - numpy==1.24.4 + - oauthlib==3.2.2 + - onnx==1.12.0 + - onnxconverter-common==1.13.0 + - onnxruntime==1.15.1 + - opt-einsum==3.3.0 + - packaging==23.1 + - pandas==1.5.3 + - pbr==5.11.1 + - pep8-naming==0.10.0 + - pickydict==0.4.0 + - pillow==10.0.0 + - platformdirs==3.10.0 + - pluggy==1.3.0 + - prospector==1.10.2 + - protobuf==3.19.6 + - pubchempy==1.0.4 + - pyasn1==0.5.0 + - pyasn1-modules==0.3.0 + - pycodestyle==2.9.1 + - pydocstyle==6.3.0 + - pyflakes==2.5.0 + - pygments==2.16.1 + - pylint==2.17.5 + - pylint-celery==0.3 + - pylint-django==2.5.3 + - pylint-flask==0.6 + - pylint-plugin-utils==0.7 + - pyparsing==3.0.9 + - pyproject-hooks==1.0.0 + - pyroma==4.2 + - pyteomics==4.6 + - pytest==7.4.0 + - pytest-cov==4.1.0 + - python-dateutil==2.8.2 + - python-louvain==0.16 + - pytz==2023.3 + - pyyaml==6.0.1 + - rdkit==2023.3.3 + - requests==2.31.0 + - requests-oauthlib==1.3.1 + - requirements-detector==1.2.2 + - rsa==4.9 + - scikit-learn==1.3.0 + - scipy==1.10.1 + - semver==3.0.1 + - setoptconf-tmp==0.3.1 + - six==1.16.0 + - skl2onnx==1.15.0 + - smart-open==6.3.0 + - smmap==5.0.0 + - snowballstemmer==2.2.0 + - spec2vec==0.8.0 + - sphinx==3.5.4 + - sphinx-rtd-theme==1.3.0 + - sphinxcontrib-apidoc==0.3.0 + - sphinxcontrib-applehelp==1.0.4 + - sphinxcontrib-devhelp==1.0.2 + - sphinxcontrib-htmlhelp==2.0.1 + - sphinxcontrib-jquery==4.1 + - sphinxcontrib-jsmath==1.0.1 + - sphinxcontrib-qthelp==1.0.3 + - sphinxcontrib-serializinghtml==1.1.5 + - sympy==1.12 + - tensorboard==2.8.0 + - tensorboard-data-server==0.6.1 + - tensorboard-plugin-wit==1.8.1 + - tensorflow==2.8.4 + - tensorflow-estimator==2.8.0 + - tensorflow-io-gcs-filesystem==0.33.0 + - termcolor==2.3.0 + - threadpoolctl==3.2.0 + - toml==0.10.2 + - tomli==2.0.1 + - tomlkit==0.12.1 + - tqdm==4.66.1 + - trove-classifiers==2023.8.7 + - typing-extensions==4.7.1 + - urllib3==1.26.16 + - werkzeug==2.3.7 + - wrapt==1.15.0 + - yapf==0.40.1 + - zipp==3.16.2 From 3a875838bbff312d367bee6f55fdb04ced04072c Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Tue, 29 Aug 2023 17:43:49 +0200 Subject: [PATCH 03/28] added yml_checks to build workflow --- .github/workflows/CI_build.yml | 30 +++++++++++++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index b0e61440..88a7f77f 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -99,4 +99,32 @@ jobs: pip list - name: Run tests run: | - pytest -m "integration" \ No newline at end of file + pytest -m "integration" + yml_checks: + name: envionment.yml checks / python-${{ matrix.python-version }} / ${{ matrix.os }} + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + os: ['ubuntu-latest'] + python-version: ['3.8'] + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Python info + run: | + which python + python --version + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install environment.yml + - name: Show pip list + run: | + pip list + - name: Run tests + run: | + pytest -m "not integration" From d31156e144955d61c56541ddc4cb0d4980be4760 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Tue, 29 Aug 2023 17:46:14 +0200 Subject: [PATCH 04/28] Fix mistake in yml checks --- .github/workflows/CI_build.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 88a7f77f..d30986dd 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -121,7 +121,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install environment.yml + conda env create -f environment.yml -n ms2query + conda activate ms2query - name: Show pip list run: | pip list From 5cb96e34a10ca3db0eba509a0064b5d018e54fc6 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Tue, 29 Aug 2023 17:51:19 +0200 Subject: [PATCH 05/28] Fix mistake in yml checks --- .github/workflows/CI_build.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index d30986dd..3201f819 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -110,19 +110,19 @@ jobs: python-version: ['3.8'] steps: - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 + - name: Set up Miniconda + uses: conda-incubator/setup-miniconda@v2 with: - python-version: ${{ matrix.python-version }} + auto_update_conda: false + miniconda_version: 'latest' + - name: Install dependencies + run: | + conda env create -f environment.yml -n ms2query + conda activate ms2query - name: Python info run: | which python python --version - - name: Install dependencies - run: | - python -m pip install --upgrade pip - conda env create -f environment.yml -n ms2query - conda activate ms2query - name: Show pip list run: | pip list From 48ce3a7afa312119af192a05c9d722bd3e5d76f8 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Tue, 29 Aug 2023 17:58:29 +0200 Subject: [PATCH 06/28] Add conda init bash --- .github/workflows/CI_build.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 3201f819..db19e407 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -117,6 +117,7 @@ jobs: miniconda_version: 'latest' - name: Install dependencies run: | + conda init bash conda env create -f environment.yml -n ms2query conda activate ms2query - name: Python info From 60aec3de975082ab48394735e09a32414b13d78d Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Tue, 29 Aug 2023 18:01:42 +0200 Subject: [PATCH 07/28] add correct miniconda version and use mamba --- .github/workflows/CI_build.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index db19e407..d6bfd525 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -113,8 +113,10 @@ jobs: - name: Set up Miniconda uses: conda-incubator/setup-miniconda@v2 with: - auto_update_conda: false - miniconda_version: 'latest' + auto-update-conda: false + miniconda-version: 'latest' + use-mamba: True + mamba-version: 'latest' - name: Install dependencies run: | conda init bash From 5b5f15072fd1ee40fca77304423ad1096f3e0fb5 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Tue, 29 Aug 2023 18:09:19 +0200 Subject: [PATCH 08/28] Directly install envionment.yml --- .github/workflows/CI_build.yml | 21 ++++++--------------- 1 file changed, 6 insertions(+), 15 deletions(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index d6bfd525..1df7d5c3 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -113,22 +113,13 @@ jobs: - name: Set up Miniconda uses: conda-incubator/setup-miniconda@v2 with: - auto-update-conda: false - miniconda-version: 'latest' - use-mamba: True - mamba-version: 'latest' - - name: Install dependencies - run: | - conda init bash - conda env create -f environment.yml -n ms2query - conda activate ms2query - - name: Python info - run: | - which python - python --version - - name: Show pip list + auto-update-conda: true + environment_file: environment.yml + python-version: ${{ matrix.python-version }} + - name: Show conda list run: | - pip list + conda info + conda list - name: Run tests run: | pytest -m "not integration" From c9a27bbf6a4493d86b3fce254cf88d6bc69089ec Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Tue, 29 Aug 2023 18:10:53 +0200 Subject: [PATCH 09/28] fix typo --- .github/workflows/CI_build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 1df7d5c3..384ff2cf 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -114,7 +114,7 @@ jobs: uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true - environment_file: environment.yml + environment-file: environment.yml python-version: ${{ matrix.python-version }} - name: Show conda list run: | From 8018bf1d6e2f3c0056e7778f9fdb0459ab1b168a Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Tue, 29 Aug 2023 18:18:55 +0200 Subject: [PATCH 10/28] new fix --- .github/workflows/CI_build.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 384ff2cf..4543a9db 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -113,9 +113,10 @@ jobs: - name: Set up Miniconda uses: conda-incubator/setup-miniconda@v2 with: - auto-update-conda: true - environment-file: environment.yml - python-version: ${{ matrix.python-version }} + activate-environment: anaconda-client-env + environment-file: ./environment.yml + python-version: 3.8 + auto-activate-base: false - name: Show conda list run: | conda info From 8de38d0877a99b428541e1728e0ca2079049ed54 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 10:46:17 +0200 Subject: [PATCH 11/28] Even closer to example workflow run --- .github/workflows/CI_build.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 4543a9db..e7b0db9a 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -102,12 +102,7 @@ jobs: pytest -m "integration" yml_checks: name: envionment.yml checks / python-${{ matrix.python-version }} / ${{ matrix.os }} - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - os: ['ubuntu-latest'] - python-version: ['3.8'] + runs-on: 'ubuntu-latest' steps: - uses: actions/checkout@v2 - name: Set up Miniconda From 0e59c50c7cf19d6fb1c4d20bb51b12440d88130f Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 11:35:04 +0200 Subject: [PATCH 12/28] Remove pip installed packages from environment.yml --- environment.yml | 352 ++++++++++++++++++++++++++++-------------------- 1 file changed, 206 insertions(+), 146 deletions(-) diff --git a/environment.yml b/environment.yml index f70e018a..b64c11d3 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: ms2query +name: ms2query_conda channels: - conda-forge - bioconda @@ -6,165 +6,225 @@ channels: dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=2_gnu + - abseil-cpp=20210324.2=h9c3ff4c_0 + - absl-py=1.4.0=pyhd8ed1ab_0 + - aiohttp=3.8.5=py38h01eb140_0 + - aiosignal=1.3.1=pyhd8ed1ab_0 + - astunparse=1.6.3=pyhd8ed1ab_0 + - async-timeout=4.0.3=pyhd8ed1ab_0 + - attrs=23.1.0=pyh71513ae_1 + - blinker=1.6.2=pyhd8ed1ab_0 + - boost=1.78.0=py38h4e30db6_4 + - boost-cpp=1.78.0=h5adbc97_2 + - brotli=1.0.9=h166bdaf_9 + - brotli-bin=1.0.9=h166bdaf_9 + - brotli-python=1.0.9=py38hfa26641_9 - bzip2=1.0.8=h7f98852_4 + - c-ares=1.19.1=hd590300_0 - ca-certificates=2023.7.22=hbcca054_0 + - cached-property=1.5.2=hd8ed1ab_1 + - cached_property=1.5.2=pyha770c72_1 + - cachetools=5.3.1=pyhd8ed1ab_0 + - cairo=1.16.0=ha61ee94_1014 + - certifi=2023.7.22=pyhd8ed1ab_0 + - cffi=1.15.1=py38h4a40e3a_3 + - charset-normalizer=3.2.0=pyhd8ed1ab_0 + - click=8.1.7=unix_pyh707e725_0 + - colorama=0.4.6=pyhd8ed1ab_0 + - coloredlogs=15.0.1=pyhd8ed1ab_3 + - contourpy=1.1.0=py38h7f3f72f_0 + - cryptography=39.0.0=py38h1724139_0 + - cycler=0.11.0=pyhd8ed1ab_0 + - deprecated=1.2.14=pyh1a96a4e_0 + - exceptiongroup=1.1.3=pyhd8ed1ab_0 + - expat=2.5.0=hcb278e6_1 + - font-ttf-dejavu-sans-mono=2.37=hab24e00_0 + - font-ttf-inconsolata=3.000=h77eed37_0 + - font-ttf-source-code-pro=2.038=h77eed37_0 + - font-ttf-ubuntu=0.83=hab24e00_0 + - fontconfig=2.14.2=h14ed4e7_0 + - fonts-conda-ecosystem=1=0 + - fonts-conda-forge=1=0 + - fonttools=4.42.1=py38h01eb140_0 + - freetype=2.12.1=hca18f0e_1 + - freetype-py=2.3.0=pyhd8ed1ab_0 + - frozenlist=1.4.0=py38h01eb140_0 + - fst-pso=1.8.1=pyhd8ed1ab_0 + - fuzzytm=2.0.5=pyhd8ed1ab_0 + - gast=0.5.4=pyhd8ed1ab_0 + - gensim=4.3.2=py38h53bb729_0 + - gettext=0.21.1=h27087fc_0 + - giflib=5.2.1=h0b41bf4_3 + - gmp=6.2.1=h58526e2_0 + - gmpy2=2.1.2=py38h793c122_1 + - google-auth=2.17.3=pyh1a96a4e_0 + - google-auth-oauthlib=0.4.6=pyhd8ed1ab_0 + - google-pasta=0.2.0=pyh8c360ce_0 + - greenlet=2.0.2=py38h17151c0_1 + - grpc-cpp=1.45.2=h9d3bbbb_5 + - grpcio=1.45.0=py38ha0cdfde_0 + - h5py=3.9.0=nompi_py38h89e2d6c_100 + - hdf5=1.14.0=nompi_h5231ba7_103 + - humanfriendly=10.0=py38h578d9bd_4 + - icu=70.1=h27087fc_0 + - idna=3.4=pyhd8ed1ab_0 + - importlib-metadata=6.8.0=pyha770c72_0 + - importlib-resources=6.0.1=pyhd8ed1ab_0 + - importlib_resources=6.0.1=pyhd8ed1ab_0 + - iniconfig=2.0.0=pyhd8ed1ab_0 + - joblib=1.3.2=pyhd8ed1ab_0 + - jpeg=9e=h0b41bf4_3 + - keras=2.8.0=pyhd8ed1ab_0 + - keras-preprocessing=1.1.2=pyhd8ed1ab_0 + - keyutils=1.6.1=h166bdaf_0 + - kiwisolver=1.4.5=py38h7f3f72f_0 + - krb5=1.20.1=hf9c8cef_0 + - lcms2=2.15=hfd0df8a_0 - ld_impl_linux-64=2.40=h41732ed_0 + - lerc=4.0.0=h27087fc_0 + - libaec=1.0.6=hcb278e6_1 + - libblas=3.9.0=17_linux64_openblas + - libbrotlicommon=1.0.9=h166bdaf_9 + - libbrotlidec=1.0.9=h166bdaf_9 + - libbrotlienc=1.0.9=h166bdaf_9 + - libcblas=3.9.0=17_linux64_openblas + - libcurl=7.87.0=h6312ad2_0 + - libdeflate=1.17=h0b41bf4_0 + - libedit=3.1.20191231=he28a2e2_2 + - libev=4.33=h516909a_1 + - libexpat=2.5.0=hcb278e6_1 - libffi=3.4.2=h7f98852_5 - libgcc-ng=13.1.0=he5830b7_0 + - libgfortran-ng=13.1.0=h69a702a_0 + - libgfortran5=13.1.0=h15d22d2_0 + - libglib=2.76.4=hebfc3b9_0 - libgomp=13.1.0=he5830b7_0 + - libiconv=1.17=h166bdaf_0 + - liblapack=3.9.0=17_linux64_openblas + - libllvm14=14.0.6=hcd5def8_4 + - libnghttp2=1.51.0=hdcd2b5c_0 - libnsl=2.0.0=h7f98852_0 + - libopenblas=0.3.23=pthreads_h80387f5_0 + - libpng=1.6.39=h753d276_0 + - libprotobuf=3.20.3=h3eb15da_0 - libsqlite=3.43.0=h2797004_0 + - libssh2=1.10.0=haa6b8db_3 + - libstdcxx-ng=13.1.0=hfd8a6a1_0 + - libtiff=4.5.0=h6adf6a1_2 - libuuid=2.38.1=h0b41bf4_0 + - libwebp-base=1.3.1=hd590300_0 + - libxcb=1.13=h7f98852_1004 + - libxml2=2.10.3=hca2bb57_4 + - libxslt=1.1.37=h873f0b0_0 - libzlib=1.2.13=hd590300_5 + - llvmlite=0.40.1=py38h94a1851_0 + - lxml=4.9.2=py38h215a2d7_0 + - markdown=3.4.4=pyhd8ed1ab_0 + - markupsafe=2.1.3=py38h01eb140_0 + - matchms=0.17.0=pyh7cba7a3_0 + - matchmsextras=0.4.1=pyhdfd78af_0 + - matplotlib-base=3.7.2=py38hf5b0b65_0 + - miniful=0.0.6=pyhd8ed1ab_0 + - mpc=1.3.1=hfe3b2da_0 + - mpfr=4.2.0=hb012696_0 + - mpmath=1.3.0=pyhd8ed1ab_0 + - ms2deepscore=0.4.0=pyhdfd78af_0 + - ms2query=1.2.2=pyhdfd78af_0 + - multidict=6.0.4=py38h1de0b5d_0 + - munkres=1.1.4=pyh9f0ad1d_0 - ncurses=6.4=hcb278e6_0 - - openssl=3.1.2=hd590300_0 + - networkx=3.1=pyhd8ed1ab_0 + - numba=0.57.1=py38hd559b08_0 + - numpy=1.24.4=py38h59b608b_0 + - oauthlib=3.2.2=pyhd8ed1ab_0 + - onnx=1.12.0=py38h8d49f1e_0 + - onnxconverter-common=1.13.0=pyhd8ed1ab_0 + - onnxruntime=1.15.1=py38h896e202_2_cpu + - openjpeg=2.5.0=hfec8fc6_2 + - openssl=1.1.1v=hd590300_0 + - opt_einsum=3.3.0=pyhd8ed1ab_1 + - packaging=23.1=pyhd8ed1ab_0 + - pandas=1.5.3=py38hdc8b05c_1 + - pcre2=10.40=hc3806b6_0 + - pickydict=0.4.0=pyhd8ed1ab_0 + - pillow=9.4.0=py38hde6dc18_1 - pip=23.2.1=pyhd8ed1ab_0 - - python=3.8.17=he550d4f_0_cpython + - pixman=0.40.0=h36c2ea0_0 + - platformdirs=3.10.0=pyhd8ed1ab_0 + - pluggy=1.3.0=pyhd8ed1ab_0 + - pooch=1.7.0=pyha770c72_3 + - protobuf=3.20.3=py38h8dc9893_1 + - pthread-stubs=0.4=h36c2ea0_1001 + - pubchempy=1.0.4=py_0 + - pyasn1=0.4.8=py_0 + - pyasn1-modules=0.2.7=py_0 + - pycairo=1.24.0=py38h1a1917b_0 + - pycparser=2.21=pyhd8ed1ab_0 + - pyfume=0.2.25=pyhd8ed1ab_0 + - pyjwt=2.8.0=pyhd8ed1ab_0 + - pyopenssl=23.2.0=pyhd8ed1ab_1 + - pyparsing=3.0.9=pyhd8ed1ab_0 + - pysocks=1.7.1=pyha2e5f31_6 + - pyteomics=4.6=pyh7cba7a3_0 + - pytest=7.4.0=pyhd8ed1ab_0 + - python=3.8.15=h257c98d_0_cpython + - python-dateutil=2.8.2=pyhd8ed1ab_0 + - python-flatbuffers=23.5.26=pyhd8ed1ab_0 + - python-louvain=0.16=pyhd8ed1ab_0 + - python_abi=3.8=3_cp38 + - pytz=2023.3=pyhd8ed1ab_0 + - pyu2f=0.1.5=pyhd8ed1ab_0 + - rdkit=2023.03.3=py38h36d2b2f_0 + - re2=2022.06.01=h27087fc_1 - readline=8.2=h8228510_1 + - reportlab=4.0.4=py38h01eb140_0 + - requests=2.31.0=pyhd8ed1ab_0 + - requests-oauthlib=1.3.1=pyhd8ed1ab_0 + - rlpycairo=0.2.0=pyhd8ed1ab_0 + - rsa=4.9=pyhd8ed1ab_0 + - scikit-learn=1.3.0=py38hc099248_0 + - scipy=1.10.1=py38h59b608b_3 - setuptools=68.1.2=pyhd8ed1ab_0 + - simpful=2.11.0=pyhd8ed1ab_0 + - six=1.16.0=pyh6c4a22f_0 + - skl2onnx=1.15.0=pyhd8ed1ab_0 + - smart_open=6.3.0=pyhd8ed1ab_1 + - snappy=1.1.10=h9fff704_0 + - spec2vec=0.8.0=pyhdfd78af_0 + - sqlalchemy=2.0.20=py38h01eb140_0 + - sqlite=3.43.0=h2c6b66d_0 + - sympy=1.12=pypyh9d50eac_103 + - tensorboard=2.8.0=pyhd8ed1ab_1 + - tensorboard-data-server=0.6.1=py38h2b5fc30_4 + - tensorboard-plugin-wit=1.8.1=pyhd8ed1ab_0 + - tensorflow=2.8.1=cpu_py38h66f0ec1_0 + - tensorflow-base=2.8.1=cpu_py38hc7a75a0_0 + - tensorflow-estimator=2.8.1=cpu_py38h4e23bc6_0 + - termcolor=2.3.0=pyhd8ed1ab_0 + - threadpoolctl=3.2.0=pyha21a80b_0 - tk=8.6.12=h27826a3_0 + - tomli=2.0.1=pyhd8ed1ab_0 + - tqdm=4.66.1=pyhd8ed1ab_0 + - typing-extensions=4.7.1=hd8ed1ab_0 + - typing_extensions=4.7.1=pyha770c72_0 + - unicodedata2=15.0.0=py38h0a891b7_0 + - urllib3=2.0.4=pyhd8ed1ab_0 + - werkzeug=2.3.7=pyhd8ed1ab_0 - wheel=0.41.2=pyhd8ed1ab_0 + - wrapt=1.15.0=py38h1de0b5d_0 + - xorg-kbproto=1.0.7=h7f98852_1002 + - xorg-libice=1.1.1=hd590300_0 + - xorg-libsm=1.2.4=h7391055_0 + - xorg-libx11=1.8.4=h0b41bf4_0 + - xorg-libxau=1.0.11=hd590300_0 + - xorg-libxdmcp=1.1.3=h7f98852_0 + - xorg-libxext=1.3.4=h0b41bf4_2 + - xorg-libxrender=0.9.10=h7f98852_1003 + - xorg-renderproto=0.11.1=h7f98852_1002 + - xorg-xextproto=7.3.0=h0b41bf4_1003 + - xorg-xproto=7.0.31=h7f98852_1007 - xz=5.2.6=h166bdaf_0 - - pip: - - absl-py==1.4.0 - - alabaster==0.7.13 - - astroid==2.15.6 - - astunparse==1.6.3 - - babel==2.12.1 - - build==0.10.0 - - bump2version==1.0.1 - - cachetools==5.3.1 - - certifi==2023.7.22 - - charset-normalizer==3.2.0 - - coloredlogs==15.0.1 - - contourpy==1.1.0 - - coverage==7.3.0 - - cycler==0.11.0 - - deprecated==1.2.14 - - dill==0.3.7 - - docutils==0.16 - - dodgy==0.2.1 - - exceptiongroup==1.1.3 - - flake8==5.0.4 - - flake8-polyfill==1.0.2 - - flatbuffers==23.5.26 - - fonttools==4.42.1 - - gast==0.5.4 - - gensim==4.3.2 - - gitdb==4.0.10 - - gitpython==3.1.32 - - google-auth==2.22.0 - - google-auth-oauthlib==0.4.6 - - google-pasta==0.2.0 - - grpcio==1.57.0 - - h5py==3.9.0 - - humanfriendly==10.0 - - idna==3.4 - - imagesize==1.4.1 - - importlib-metadata==6.8.0 - - importlib-resources==6.0.1 - - iniconfig==2.0.0 - - isort==5.12.0 - - jinja2==3.1.2 - - joblib==1.3.2 - - keras==2.8.0 - - keras-preprocessing==1.1.2 - - kiwisolver==1.4.5 - - lazy-object-proxy==1.9.0 - - libclang==16.0.6 - - llvmlite==0.40.1 - - lxml==4.9.3 - - markdown==3.4.4 - - markupsafe==2.1.3 - - matchms==0.17.0 - - matchmsextras==0.4.0 - - matplotlib==3.7.2 - - mccabe==0.7.0 - - mpmath==1.3.0 - - ms2deepscore==0.4.0 - - ms2query==1.2.2 - - networkx==3.1 - - numba==0.57.1 - - numpy==1.24.4 - - oauthlib==3.2.2 - - onnx==1.12.0 - - onnxconverter-common==1.13.0 - - onnxruntime==1.15.1 - - opt-einsum==3.3.0 - - packaging==23.1 - - pandas==1.5.3 - - pbr==5.11.1 - - pep8-naming==0.10.0 - - pickydict==0.4.0 - - pillow==10.0.0 - - platformdirs==3.10.0 - - pluggy==1.3.0 - - prospector==1.10.2 - - protobuf==3.19.6 - - pubchempy==1.0.4 - - pyasn1==0.5.0 - - pyasn1-modules==0.3.0 - - pycodestyle==2.9.1 - - pydocstyle==6.3.0 - - pyflakes==2.5.0 - - pygments==2.16.1 - - pylint==2.17.5 - - pylint-celery==0.3 - - pylint-django==2.5.3 - - pylint-flask==0.6 - - pylint-plugin-utils==0.7 - - pyparsing==3.0.9 - - pyproject-hooks==1.0.0 - - pyroma==4.2 - - pyteomics==4.6 - - pytest==7.4.0 - - pytest-cov==4.1.0 - - python-dateutil==2.8.2 - - python-louvain==0.16 - - pytz==2023.3 - - pyyaml==6.0.1 - - rdkit==2023.3.3 - - requests==2.31.0 - - requests-oauthlib==1.3.1 - - requirements-detector==1.2.2 - - rsa==4.9 - - scikit-learn==1.3.0 - - scipy==1.10.1 - - semver==3.0.1 - - setoptconf-tmp==0.3.1 - - six==1.16.0 - - skl2onnx==1.15.0 - - smart-open==6.3.0 - - smmap==5.0.0 - - snowballstemmer==2.2.0 - - spec2vec==0.8.0 - - sphinx==3.5.4 - - sphinx-rtd-theme==1.3.0 - - sphinxcontrib-apidoc==0.3.0 - - sphinxcontrib-applehelp==1.0.4 - - sphinxcontrib-devhelp==1.0.2 - - sphinxcontrib-htmlhelp==2.0.1 - - sphinxcontrib-jquery==4.1 - - sphinxcontrib-jsmath==1.0.1 - - sphinxcontrib-qthelp==1.0.3 - - sphinxcontrib-serializinghtml==1.1.5 - - sympy==1.12 - - tensorboard==2.8.0 - - tensorboard-data-server==0.6.1 - - tensorboard-plugin-wit==1.8.1 - - tensorflow==2.8.4 - - tensorflow-estimator==2.8.0 - - tensorflow-io-gcs-filesystem==0.33.0 - - termcolor==2.3.0 - - threadpoolctl==3.2.0 - - toml==0.10.2 - - tomli==2.0.1 - - tomlkit==0.12.1 - - tqdm==4.66.1 - - trove-classifiers==2023.8.7 - - typing-extensions==4.7.1 - - urllib3==1.26.16 - - werkzeug==2.3.7 - - wrapt==1.15.0 - - yapf==0.40.1 - - zipp==3.16.2 + - yarl=1.9.2=py38h01eb140_0 + - zipp=3.16.2=pyhd8ed1ab_0 + - zlib=1.2.13=hd590300_5 + - zstd=1.5.5=hfc55251_0 From 8d30254ce13c1d1e8a17905f0ea9162e8764e4cf Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 11:35:31 +0200 Subject: [PATCH 13/28] Add bioconda and conda-forge channel to CI-build --- .github/workflows/CI_build.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index e7b0db9a..ae93cd8c 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -110,6 +110,7 @@ jobs: with: activate-environment: anaconda-client-env environment-file: ./environment.yml + channels: conda-forge,bioconda python-version: 3.8 auto-activate-base: false - name: Show conda list From fcab47d3fdde0b09ff2c3d32de7e6c694b3205a8 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 11:50:49 +0200 Subject: [PATCH 14/28] Add conda activate environment --- .github/workflows/CI_build.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index ae93cd8c..3bf50420 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -110,9 +110,10 @@ jobs: with: activate-environment: anaconda-client-env environment-file: ./environment.yml - channels: conda-forge,bioconda python-version: 3.8 - auto-activate-base: false + auto-activate-base: False + - name: Activate Conda environment + run: conda activate anaconda-client-env - name: Show conda list run: | conda info From 7a9475468329dc1850230ccd24e7f7528c37dc4a Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 11:54:22 +0200 Subject: [PATCH 15/28] Add activate ms2query --- .github/workflows/CI_build.yml | 5 +---- environment.yml | 2 +- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 3bf50420..67d39687 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -108,12 +108,9 @@ jobs: - name: Set up Miniconda uses: conda-incubator/setup-miniconda@v2 with: - activate-environment: anaconda-client-env + activate-environment: ms2query environment-file: ./environment.yml python-version: 3.8 - auto-activate-base: False - - name: Activate Conda environment - run: conda activate anaconda-client-env - name: Show conda list run: | conda info diff --git a/environment.yml b/environment.yml index b64c11d3..ac1d527a 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: ms2query_conda +name: ms2query channels: - conda-forge - bioconda From 5c20b610c47d4c011a5c04d5cf74ee8c66af5fdc Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 12:08:12 +0200 Subject: [PATCH 16/28] Activate ms2query --- .github/workflows/CI_build.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 67d39687..b6123d06 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -111,6 +111,9 @@ jobs: activate-environment: ms2query environment-file: ./environment.yml python-version: 3.8 + - name: activate conda environment + run: | + conda activate ms2query - name: Show conda list run: | conda info From 1380544bbda69a42bedace61275084341257e808 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 13:03:35 +0200 Subject: [PATCH 17/28] Add shell: bash -l {0} --- .github/workflows/CI_build.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index b6123d06..91349077 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -113,6 +113,7 @@ jobs: python-version: 3.8 - name: activate conda environment run: | + shell: bash -l {0} conda activate ms2query - name: Show conda list run: | From c23538d9710f74253059ea6df693908ad16d8041 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 13:15:09 +0200 Subject: [PATCH 18/28] Add shell: bash -l {0} defaults --- .github/workflows/CI_build.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 91349077..25915d46 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -103,6 +103,9 @@ jobs: yml_checks: name: envionment.yml checks / python-${{ matrix.python-version }} / ${{ matrix.os }} runs-on: 'ubuntu-latest' + defaults: + run: + shell: bash -el {0} steps: - uses: actions/checkout@v2 - name: Set up Miniconda @@ -113,7 +116,6 @@ jobs: python-version: 3.8 - name: activate conda environment run: | - shell: bash -l {0} conda activate ms2query - name: Show conda list run: | From 817955b313a162de08c6eedcbe72fa778441598b Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 13:17:56 +0200 Subject: [PATCH 19/28] Add shell: bash -l {0} defaults --- .github/workflows/CI_build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 25915d46..020f9a5a 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -105,7 +105,7 @@ jobs: runs-on: 'ubuntu-latest' defaults: run: - shell: bash -el {0} + shell: sh -l {0} steps: - uses: actions/checkout@v2 - name: Set up Miniconda From c0f2fc57daf1cb92ebd4acdf947f78eef524109b Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 13:25:52 +0200 Subject: [PATCH 20/28] Change to shell: bash --- .github/workflows/CI_build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 020f9a5a..3cf1eda6 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -105,7 +105,7 @@ jobs: runs-on: 'ubuntu-latest' defaults: run: - shell: sh -l {0} + shell: bash steps: - uses: actions/checkout@v2 - name: Set up Miniconda From 193b97a1cec050fdda6752e8edee44b682b83e56 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 13:33:00 +0200 Subject: [PATCH 21/28] Change to shell: bash --- .github/workflows/CI_build.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 3cf1eda6..701a82cc 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -116,6 +116,7 @@ jobs: python-version: 3.8 - name: activate conda environment run: | + conda init bash conda activate ms2query - name: Show conda list run: | From bff9ece7304c059cc96d1ebcbf429ae27b4061d0 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 13:45:20 +0200 Subject: [PATCH 22/28] Update bashrc --- .github/workflows/CI_build.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 701a82cc..44b36000 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -116,7 +116,8 @@ jobs: python-version: 3.8 - name: activate conda environment run: | - conda init bash + echo "source $CONDA_PREFIX/etc/profile.d/conda.sh" >> ~/.bashrc + source ~/.bashrc conda activate ms2query - name: Show conda list run: | @@ -124,4 +125,4 @@ jobs: conda list - name: Run tests run: | - pytest -m "not integration" + pytest -m "not integration" \ No newline at end of file From 3613796615189fc69a678b79aebb2f12ecf537c1 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 13:55:36 +0200 Subject: [PATCH 23/28] Use bash -l {0} --- .github/workflows/CI_build.yml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 44b36000..a5529a6c 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -103,9 +103,6 @@ jobs: yml_checks: name: envionment.yml checks / python-${{ matrix.python-version }} / ${{ matrix.os }} runs-on: 'ubuntu-latest' - defaults: - run: - shell: bash steps: - uses: actions/checkout@v2 - name: Set up Miniconda @@ -115,11 +112,11 @@ jobs: environment-file: ./environment.yml python-version: 3.8 - name: activate conda environment + shell: bash -l {0} run: | - echo "source $CONDA_PREFIX/etc/profile.d/conda.sh" >> ~/.bashrc - source ~/.bashrc conda activate ms2query - name: Show conda list + shell: bash -l {0} run: | conda info conda list From 1528c9064193e503f0d60a805ab97fd2fdd9f40d Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 14:04:18 +0200 Subject: [PATCH 24/28] Use bash -l {0} in run tests as well --- .github/workflows/CI_build.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index a5529a6c..3d18bb35 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -105,6 +105,7 @@ jobs: runs-on: 'ubuntu-latest' steps: - uses: actions/checkout@v2 + - defaults - name: Set up Miniconda uses: conda-incubator/setup-miniconda@v2 with: @@ -121,5 +122,7 @@ jobs: conda info conda list - name: Run tests + shell: bash -l {0} run: | + conda activate ms2query pytest -m "not integration" \ No newline at end of file From 0fa92ab5b38dbbddac3410b4b131a8f0d776cab7 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 14:06:21 +0200 Subject: [PATCH 25/28] removed accidental defaults --- .github/workflows/CI_build.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index 3d18bb35..f9e668ff 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -105,7 +105,6 @@ jobs: runs-on: 'ubuntu-latest' steps: - uses: actions/checkout@v2 - - defaults - name: Set up Miniconda uses: conda-incubator/setup-miniconda@v2 with: From 9a79b08dda1e0ba880fc39ed6c46809a67475a4e Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 14:13:14 +0200 Subject: [PATCH 26/28] Simplify CI run --- .github/workflows/CI_build.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/CI_build.yml b/.github/workflows/CI_build.yml index f9e668ff..b6a1d1ed 100644 --- a/.github/workflows/CI_build.yml +++ b/.github/workflows/CI_build.yml @@ -102,6 +102,9 @@ jobs: pytest -m "integration" yml_checks: name: envionment.yml checks / python-${{ matrix.python-version }} / ${{ matrix.os }} + defaults: + run: + shell: bash -l {0} runs-on: 'ubuntu-latest' steps: - uses: actions/checkout@v2 @@ -112,16 +115,12 @@ jobs: environment-file: ./environment.yml python-version: 3.8 - name: activate conda environment - shell: bash -l {0} run: | conda activate ms2query - name: Show conda list - shell: bash -l {0} run: | conda info conda list - name: Run tests - shell: bash -l {0} run: | - conda activate ms2query pytest -m "not integration" \ No newline at end of file From e14250189ce1f81eaadf9d3b932319dd9a90b7f4 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 14:20:13 +0200 Subject: [PATCH 27/28] Update CHANGELOG.md --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1dbb7ce7..23524cfe 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,10 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## unpublished +### Added +- environment.yml and CI_build test fur building a conda env from this file + ## 1.2.2 ### fixed - Set version of matchmsextras to 0.4.0, to fix dependency issue From bb6399b99fba5e0b8e7486b9974634b59baf13d7 Mon Sep 17 00:00:00 2001 From: niekdejonge Date: Wed, 30 Aug 2023 14:28:55 +0200 Subject: [PATCH 28/28] Add missing stuff after merge --- environment.yml | 111 +++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 110 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 3e2988e0..ac1d527a 100644 --- a/environment.yml +++ b/environment.yml @@ -6,7 +6,21 @@ channels: dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=2_gnu + - abseil-cpp=20210324.2=h9c3ff4c_0 + - absl-py=1.4.0=pyhd8ed1ab_0 + - aiohttp=3.8.5=py38h01eb140_0 + - aiosignal=1.3.1=pyhd8ed1ab_0 + - astunparse=1.6.3=pyhd8ed1ab_0 + - async-timeout=4.0.3=pyhd8ed1ab_0 + - attrs=23.1.0=pyh71513ae_1 + - blinker=1.6.2=pyhd8ed1ab_0 + - boost=1.78.0=py38h4e30db6_4 + - boost-cpp=1.78.0=h5adbc97_2 + - brotli=1.0.9=h166bdaf_9 + - brotli-bin=1.0.9=h166bdaf_9 + - brotli-python=1.0.9=py38hfa26641_9 - bzip2=1.0.8=h7f98852_4 + - c-ares=1.19.1=hd590300_0 - ca-certificates=2023.7.22=hbcca054_0 - cached-property=1.5.2=hd8ed1ab_1 - cached_property=1.5.2=pyha770c72_1 @@ -66,6 +80,43 @@ dependencies: - kiwisolver=1.4.5=py38h7f3f72f_0 - krb5=1.20.1=hf9c8cef_0 - lcms2=2.15=hfd0df8a_0 + - ld_impl_linux-64=2.40=h41732ed_0 + - lerc=4.0.0=h27087fc_0 + - libaec=1.0.6=hcb278e6_1 + - libblas=3.9.0=17_linux64_openblas + - libbrotlicommon=1.0.9=h166bdaf_9 + - libbrotlidec=1.0.9=h166bdaf_9 + - libbrotlienc=1.0.9=h166bdaf_9 + - libcblas=3.9.0=17_linux64_openblas + - libcurl=7.87.0=h6312ad2_0 + - libdeflate=1.17=h0b41bf4_0 + - libedit=3.1.20191231=he28a2e2_2 + - libev=4.33=h516909a_1 + - libexpat=2.5.0=hcb278e6_1 + - libffi=3.4.2=h7f98852_5 + - libgcc-ng=13.1.0=he5830b7_0 + - libgfortran-ng=13.1.0=h69a702a_0 + - libgfortran5=13.1.0=h15d22d2_0 + - libglib=2.76.4=hebfc3b9_0 + - libgomp=13.1.0=he5830b7_0 + - libiconv=1.17=h166bdaf_0 + - liblapack=3.9.0=17_linux64_openblas + - libllvm14=14.0.6=hcd5def8_4 + - libnghttp2=1.51.0=hdcd2b5c_0 + - libnsl=2.0.0=h7f98852_0 + - libopenblas=0.3.23=pthreads_h80387f5_0 + - libpng=1.6.39=h753d276_0 + - libprotobuf=3.20.3=h3eb15da_0 + - libsqlite=3.43.0=h2797004_0 + - libssh2=1.10.0=haa6b8db_3 + - libstdcxx-ng=13.1.0=hfd8a6a1_0 + - libtiff=4.5.0=h6adf6a1_2 + - libuuid=2.38.1=h0b41bf4_0 + - libwebp-base=1.3.1=hd590300_0 + - libxcb=1.13=h7f98852_1004 + - libxml2=2.10.3=hca2bb57_4 + - libxslt=1.1.37=h873f0b0_0 + - libzlib=1.2.13=hd590300_5 - llvmlite=0.40.1=py38h94a1851_0 - lxml=4.9.2=py38h215a2d7_0 - markdown=3.4.4=pyhd8ed1ab_0 @@ -81,6 +132,23 @@ dependencies: - ms2query=1.2.2=pyhdfd78af_0 - multidict=6.0.4=py38h1de0b5d_0 - munkres=1.1.4=pyh9f0ad1d_0 + - ncurses=6.4=hcb278e6_0 + - networkx=3.1=pyhd8ed1ab_0 + - numba=0.57.1=py38hd559b08_0 + - numpy=1.24.4=py38h59b608b_0 + - oauthlib=3.2.2=pyhd8ed1ab_0 + - onnx=1.12.0=py38h8d49f1e_0 + - onnxconverter-common=1.13.0=pyhd8ed1ab_0 + - onnxruntime=1.15.1=py38h896e202_2_cpu + - openjpeg=2.5.0=hfec8fc6_2 + - openssl=1.1.1v=hd590300_0 + - opt_einsum=3.3.0=pyhd8ed1ab_1 + - packaging=23.1=pyhd8ed1ab_0 + - pandas=1.5.3=py38hdc8b05c_1 + - pcre2=10.40=hc3806b6_0 + - pickydict=0.4.0=pyhd8ed1ab_0 + - pillow=9.4.0=py38hde6dc18_1 + - pip=23.2.1=pyhd8ed1ab_0 - pixman=0.40.0=h36c2ea0_0 - platformdirs=3.10.0=pyhd8ed1ab_0 - pluggy=1.3.0=pyhd8ed1ab_0 @@ -108,6 +176,33 @@ dependencies: - pyu2f=0.1.5=pyhd8ed1ab_0 - rdkit=2023.03.3=py38h36d2b2f_0 - re2=2022.06.01=h27087fc_1 + - readline=8.2=h8228510_1 + - reportlab=4.0.4=py38h01eb140_0 + - requests=2.31.0=pyhd8ed1ab_0 + - requests-oauthlib=1.3.1=pyhd8ed1ab_0 + - rlpycairo=0.2.0=pyhd8ed1ab_0 + - rsa=4.9=pyhd8ed1ab_0 + - scikit-learn=1.3.0=py38hc099248_0 + - scipy=1.10.1=py38h59b608b_3 + - setuptools=68.1.2=pyhd8ed1ab_0 + - simpful=2.11.0=pyhd8ed1ab_0 + - six=1.16.0=pyh6c4a22f_0 + - skl2onnx=1.15.0=pyhd8ed1ab_0 + - smart_open=6.3.0=pyhd8ed1ab_1 + - snappy=1.1.10=h9fff704_0 + - spec2vec=0.8.0=pyhdfd78af_0 + - sqlalchemy=2.0.20=py38h01eb140_0 + - sqlite=3.43.0=h2c6b66d_0 + - sympy=1.12=pypyh9d50eac_103 + - tensorboard=2.8.0=pyhd8ed1ab_1 + - tensorboard-data-server=0.6.1=py38h2b5fc30_4 + - tensorboard-plugin-wit=1.8.1=pyhd8ed1ab_0 + - tensorflow=2.8.1=cpu_py38h66f0ec1_0 + - tensorflow-base=2.8.1=cpu_py38hc7a75a0_0 + - tensorflow-estimator=2.8.1=cpu_py38h4e23bc6_0 + - termcolor=2.3.0=pyhd8ed1ab_0 + - threadpoolctl=3.2.0=pyha21a80b_0 + - tk=8.6.12=h27826a3_0 - tomli=2.0.1=pyhd8ed1ab_0 - tqdm=4.66.1=pyhd8ed1ab_0 - typing-extensions=4.7.1=hd8ed1ab_0 @@ -115,7 +210,21 @@ dependencies: - unicodedata2=15.0.0=py38h0a891b7_0 - urllib3=2.0.4=pyhd8ed1ab_0 - werkzeug=2.3.7=pyhd8ed1ab_0 + - wheel=0.41.2=pyhd8ed1ab_0 + - wrapt=1.15.0=py38h1de0b5d_0 + - xorg-kbproto=1.0.7=h7f98852_1002 + - xorg-libice=1.1.1=hd590300_0 + - xorg-libsm=1.2.4=h7391055_0 + - xorg-libx11=1.8.4=h0b41bf4_0 + - xorg-libxau=1.0.11=hd590300_0 + - xorg-libxdmcp=1.1.3=h7f98852_0 + - xorg-libxext=1.3.4=h0b41bf4_2 + - xorg-libxrender=0.9.10=h7f98852_1003 + - xorg-renderproto=0.11.1=h7f98852_1002 + - xorg-xextproto=7.3.0=h0b41bf4_1003 + - xorg-xproto=7.0.31=h7f98852_1007 + - xz=5.2.6=h166bdaf_0 - yarl=1.9.2=py38h01eb140_0 - zipp=3.16.2=pyhd8ed1ab_0 - zlib=1.2.13=hd590300_5 - - zstd=1.5.5=hfc55251_0 \ No newline at end of file + - zstd=1.5.5=hfc55251_0