Add Dockerfile and requirements.txt

.dockerignore

@@ -0,0 +1,21 @@
+venv*
+.git
+*.egg-info
+build
+dist
+documentation
+__pycache__
+sample_data
+tests
+utils
+*.pyc
+*.pyo
+*.pyd
+.Python
+.mypy_cache
+.pytest_cache
+.hypothesis
+.tox
+.coverage
+.coverage.*
+.cache

.github/workflows/main.yml

@@ -14,11 +14,23 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v1
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          python-version: 3.9
+      - name: Update and install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            gcc \
+            g++ \
+            make \
+            libgnutls28-dev \
+            libcurl4-gnutls-dev \
+            python3-pycurl \
+            libcurl4-openssl-dev \
+            libssl-dev
       - name: Install pipenv
         uses: dschep/install-pipenv-action@v1
       - name: Install dependencies

Dockerfile

@@ -0,0 +1,15 @@
+FROM python:3.7
+
+RUN mkdir -p /app
+WORKDIR /app
+
+COPY requirements.txt .
+RUN pip install -r requirements.txt
+
+COPY setup.py .
+COPY setup.cfg .
+COPY xirt/ xirt/
+
+RUN pip install .
+
+ENTRYPOINT ["python", "-m", "xirt"]

Dockerfile-slim

@@ -0,0 +1,23 @@
+FROM python:3.7-slim
+
+RUN apt-get update && apt-get install -y \
+    gcc \
+    g++ \
+    make \
+    libgnutls28-dev \
+    libcurl4-gnutls-dev \
+    python3-pycurl \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN mkdir -p /app
+WORKDIR /app
+
+COPY setup.py .
+COPY setup.cfg .
+COPY xirt/ xirt/
+COPY requirements.txt .
+
+RUN pip install -r requirements.txt
+RUN pip install .
+
+ENTRYPOINT ["python", "-m", "xirt"]

Pipfile

@@ -7,7 +7,7 @@ name = "pypi"
 numpy = "*"
 pandas = "*"
 pyteomics = "*"
-sklearn = "*"
+scikit-learn = "*"
 tensorflow = "*"
 tensorflow_addons = "*"
 tqdm = "*"

requirements.txt

@@ -0,0 +1,149 @@
+absl-py==0.15.0
+alabaster==0.7.13
+astor==0.8.1
+astunparse==1.6.3
+atomicwrites==1.4.1
+attrs==24.2.0
+Babel==2.14.0
+backcall==0.2.0
+biopython==1.76
+cached-property==1.5.2
+cachetools==4.2.4
+certifi==2025.1.31
+charset-normalizer==3.4.1
+clang==5.0
+cloudpickle==2.2.1
+coverage==7.2.7
+cycler==0.11.0
+Cython==3.0.12
+dask==2021.7.2
+decorator==5.1.1
+deepmerge==1.1.1
+dill==0.3.7
+docutils==0.19
+et-xmlfile==1.1.0
+exceptiongroup==1.2.2
+flake8==3.9.2
+flatbuffers==1.12
+fonttools==4.38.0
+fsspec==2023.1.0
+future==1.0.0
+gast==0.4.0
+google-auth==1.35.0
+google-auth-oauthlib==0.4.6
+google-pasta==0.2.0
+graphviz==0.13.2
+grpcio==1.62.3
+h5py==3.1.0
+idna==3.10
+imagesize==1.4.1
+importlib-metadata==6.7.0
+iniconfig==2.0.0
+ipython==6.5.0
+ipython-genutils==0.2.0
+jdcal==1.4.1
+jedi==0.19.2
+Jinja2==3.1.5
+joblib==1.3.2
+keras==2.6.0
+Keras-Applications==1.0.8
+keras-nightly==2.5.0.dev2021032900
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.5
+libclang==18.1.1
+locket==1.0.0
+Markdown==3.4.4
+MarkupSafe==2.1.5
+matplotlib==3.5.3
+mccabe==0.6.1
+mdurl==0.1.2
+more-itertools==9.1.0
+multiprocess==0.70.15
+namex==0.0.8
+networkx==2.6.3
+numpy==1.19.5
+numpy-indexed==0.3.7
+numpydoc==0.8.0
+oauthlib==3.2.2
+openpyxl==2.5.6
+opt-einsum==3.3.0
+packaging==24.0
+palettable==3.3.0
+pandas==1.3.5
+parso==0.8.4
+partd==1.4.1
+pexpect==4.9.0
+pickleshare==0.7.5
+Pillow==9.5.0
+pluggy==1.2.0
+prompt-toolkit==1.0.18
+protobuf==3.19.6
+psutil==7.0.0
+ptyprocess==0.7.0
+py==1.11.0
+pyasn1==0.5.1
+pyasn1-modules==0.3.0
+pycodestyle==2.7.0
+pycurl==7.43.0.2
+pydocstyle==6.1.1
+pydot==1.4.1
+pyflakes==2.3.1
+Pygments==2.17.2
+pyparsing==3.1.4
+pyteomics==4.7.5
+pytest==7.4.4
+pytest-arraydiff==0.2
+pytest-astropy==0.4.0
+pytest-cov==4.1.0
+pytest-doctestplus==0.1.3
+pytest-flake8==1.1.0
+pytest-openfiles==0.3.0
+pytest-pydocstyle==2.3.2
+pytest-remotedata==0.3.0
+python-dateutil==2.9.0.post0
+pytz==2025.1
+PyWavelets==1.3.0
+PyYAML==6.0.1
+requests==2.31.0
+requests-oauthlib==2.0.0
+rsa==4.9
+scikit-image==0.14.2
+scikit-learn==0.22.2.post1
+scipy==1.7.3
+seaborn==0.12.2
+setuptools-scm==7.1.0
+simplegeneric==0.8.1
+six==1.15.0
+snowballstemmer==2.2.0
+Sphinx==5.3.0
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+statannot==0.2.3
+tensorboard==2.9.1
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.1
+tensorflow==2.6.0
+tensorflow-addons==0.13.0
+tensorflow-estimator==2.9.0
+tensorflow-io-gcs-filesystem==0.34.0
+termcolor==1.1.0
+tomli==2.0.1
+toolz==0.12.1
+tqdm==4.67.1
+traitlets==5.9.0
+typeguard==2.7.0
+typing-extensions==3.7.4.3
+tzdata==2025.1
+urllib3==1.23
+versioneer==0.29
+wcwidth==0.2.13
+Werkzeug==2.2.3
+wrapt==1.12.1
+xiutilities>=1.2.5
+xlrd==2.0.1
+xlwt==1.3.0
+zipp==3.15.0

requirements_fschimweg.txt

@@ -0,0 +1,68 @@
+absl-py==1.4.0
+astunparse==1.6.3
+biopython==1.81
+cachetools==5.3.1
+certifi==2023.7.22
+charset-normalizer==3.2.0
+contourpy==1.1.0
+cycler==0.11.0
+flatbuffers==23.5.26
+fonttools==4.42.0
+gast==0.4.0
+google-auth==2.22.0
+google-auth-oauthlib==1.0.0
+google-pasta==0.2.0
+graphviz==0.20.1
+grpcio==1.56.2
+h5py==3.9.0
+idna==3.4
+joblib==1.3.2
+keras==2.13.1
+Keras-Applications==1.0.8
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.4
+libclang==16.0.6
+Markdown==3.4.4
+MarkupSafe==2.1.3
+matplotlib==3.7.2
+numpy==1.24.3
+oauthlib==3.2.2
+opt-einsum==3.3.0
+packaging==23.1
+palettable==3.3.3
+pandas==2.0.3
+Pillow==10.0.0
+protobuf==4.24.0
+pyasn1==0.5.0
+pyasn1-modules==0.3.0
+pydot==1.4.2
+pyparsing==3.0.9
+pyteomics==4.6
+python-dateutil==2.8.2
+pytz==2023.3
+PyYAML==6.0.1
+requests==2.31.0
+requests-oauthlib==1.3.1
+rsa==4.9
+scikit-learn==1.3.0
+scipy==1.11.1
+seaborn==0.12.2
+six==1.16.0
+sklearn==0.0.post7
+statannot==0.2.3
+tensorboard==2.13.0
+tensorboard-data-server==0.7.1
+tensorflow==2.13.0
+tensorflow-addons==0.21.0
+tensorflow-estimator==2.13.0
+tensorflow-macos==2.13.0
+termcolor==2.3.0
+threadpoolctl==3.2.0
+tqdm==4.66.0
+typeguard==2.13.3
+typing_extensions==4.5.0
+tzdata==2023.3
+urllib3==1.26.16
+Werkzeug==2.3.6
+wrapt==1.15.0
+xlwt==1.3.0

setup.cfg

@@ -1,7 +1,7 @@
 [tool:pytest]
 pep8maxlinelength = 100
 flake8-max-line-length = 100
-addopts = --flake8 --pydocstyle --cov=xirt --cov-fail-under=90 --cov-report html --disable-warnings -n 8
+addopts = --flake8 --pydocstyle --cov=xirt --cov-fail-under=90 --cov-report html --disable-warnings
 norecursedirs = HILIC utils documentation
 
 [flake8]

setup.py

@@ -27,13 +27,18 @@
             "Chromatography", "Peptides"]
 RAPPSILBER_SOFTWARE = "https://www.rappsilberlab.org/software/"
 # What packages are required for this module to be executed?
-REQUIRED = ['numpy', 'pandas', 'tensorflow', 'seaborn', 'xlwt', 'pyyaml',
-            'pyteomics', 'sklearn', 'tqdm', 'biopython', 'palettable', 'statannot',
+REQUIRED = ['numpy', 'pandas', 'tensorflow', 'seaborn', 'xlwt', 'graphviz', 'pydot', 'pyyaml',
+            'pyteomics', 'scikit-learn', 'tqdm', 'biopython', 'pydot', 'palettable', 'statannot',
             'tensorflow_addons']
 
 # What packages are optional?
 # 'fancy feature': ['django'],}
-EXTRAS = {}
+EXTRAS = {
+    'develop': [
+        'pytest>=2.8.6',
+        'flake8>=2.5.2'
+    ]
+}
 
 # The rest you shouldn't have to touch too much :)
 # ------------------------------------------------

tests/fixtures/xirt_params_3RT.yaml

@@ -93,3 +93,10 @@ predictions:
   fractions: # simply write fractions: [] if no fraction prediction is desired
     - scx
     - hsax
+column_names:
+  peptide1_sequence: "Peptide1"
+  peptide2_sequence: "Peptide2"
+  link_pos_basename: "LinkPos"
+  peptide1_unmod_sequence: "Peptide1"
+  peptide2_unmod_sequence: "Peptide2"
+  score: "score"

tests/fixtures/xirt_params_rp.yaml

@@ -73,3 +73,10 @@ predictions:
     - rp
   # simply write fractions: [] if no fraction prediction is desired
   fractions: []
+column_names:
+  peptide1_sequence: "Peptide1"
+  peptide2_sequence: "Peptide2"
+  link_pos_basename: "LinkPos"
+  peptide1_unmod_sequence: "Peptide1"
+  peptide2_unmod_sequence: "Peptide2"
+  score: "score"

tests/fixtures/xirt_params_rp_linear.yaml

@@ -73,3 +73,10 @@ predictions:
     - rp
   # simply write fractions: [] if no fraction prediction is desired
   fractions: []
+column_names:
+  peptide1_sequence: "Peptide1"
+  peptide2_sequence: "Peptide2"
+  link_pos_basename: "LinkPos"
+  peptide1_unmod_sequence: "Peptide1"
+  peptide2_unmod_sequence: "Peptide2"
+  score: "score"

tests/fixtures/xirt_params_scx.yaml

@@ -72,3 +72,10 @@ predictions:
   continues: []
   # simply write fractions: [] if no fraction prediction is desired
   fractions: [scx]
+column_names:
+  peptide1_sequence: "Peptide1"
+  peptide2_sequence: "Peptide2"
+  link_pos_basename: "LinkPos"
+  peptide1_unmod_sequence: "Peptide1"
+  peptide2_unmod_sequence: "Peptide2"
+  score: "score"