Fix docker dependencies with pystache and fisher packages (#114)

* docs temporary workaround with old version of setuptools * fix docker with new dependencies Co-authored-by: Lonneke Scheffer <[email protected]>
uio-bmi · Nov 30, 2021 · 06ca621 · 06ca621
1 parent 7033912
commit 06ca621
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Showing 3 changed files with 11 additions and 8 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -13,16 +13,18 @@ RUN dnf install -y epel-release
 RUN dnf config-manager --set-enabled powertools
 
 # Installing yum dependencies 
-RUN yum install -y python38 python38-devel git libgit2 libgit2-devel make openssl-devel libcurl-devel libxml2-devel gcc gcc-c++ autoconf automake libtool m4 llvm llvm-devel cairo cairo-devel cairomm-devel libXt-devel
+RUN yum install -y python38 python38-devel git libgit2 libgit2-devel make openssl-devel libcurl-devel libxml2-devel gcc gcc-c++ autoconf automake libtool m4 llvm llvm-devel libXt-devel
 
 # Since we are not using venv's, we must install 'wheel' and 'setuptools' manually
-RUN pip3 install wheel setuptools cython
+RUN pip3 install wheel setuptools==50.3.2 cython
 
 # install the dependency CompAIRR
-RUN yum install git -y
 RUN git clone https://github.com/uio-bmi/compairr.git compairr_folder
 RUN make -C compairr_folder
 RUN cp ./compairr_folder/src/compairr ./compairr
 
 # Voila: install immuneML
 RUN pip3 install ./immuneML/[TCRdist]
+
+# temporary fix for ValueError due to binary incompatibilities with numpy in cfisher package (dependency for computing fisher's exact test)
+RUN pip3 install --upgrade numpy
diff --git a/requirements.txt b/requirements.txt
@@ -8,7 +8,8 @@ editdistance==0.5.3
 regex
 tzlocal
 airr>=1
-pystache
+fishersapi
+pystache==0.5.4
 torch>=1.5.1
 numpy>=1.18.5
 h5py<=2.10.0
@@ -18,7 +19,6 @@ tensorboard>=1.14.0
 requests>=2.21
 plotly>=4
 logomaker>=0.8
-Cython
-fishersapi
 matplotlib-venn>=0.11
 scipy
+Cython
diff --git a/setup.py b/setup.py
@@ -21,8 +21,9 @@ def import_requirements(filename) -> list:
     author_email="[email protected]",
     url="https://github.com/uio-bmi/immuneML",
     install_requires=["pytest>=4", "pandas>=1", "PyYAML>=5.3", "scikit-learn>=0.23", "gensim>=3.8,<4", "matplotlib>=3.1", "editdistance==0.5.3",
-                      "regex", "tzlocal", "airr>=1", "pystache", "torch>=1.5.1", "numpy>=1.18.5", "Cython", "h5py<=2.10.0", "dill>=0.3", "tqdm>=0.24", # Note: h5py v3 does not work with DeepRC, but works with everything else
-                      "tensorboard>=1.14.0", "requests>=2.21", "plotly>=4", "logomaker>=0.8", "fishersapi", "matplotlib-venn>=0.11", "scipy"],
+                      "regex", "tzlocal", "airr>=1", "pystache==0.5.4", "torch>=1.5.1", "Cython", "h5py<=2.10.0", "dill>=0.3", "tqdm>=0.24", # Note: h5py v3 does not work with DeepRC, but works with everything else
+                      "tensorboard>=1.14.0", "requests>=2.21", "plotly>=4", "logomaker>=0.8", "fishersapi", "matplotlib-venn>=0.11",
+                      "numpy>=1.18.5", "scipy"],
     extras_require={
         "TCRdist": ["parasail==1.2", "tcrdist3>=0.1.6"]
     },