fix installation & update version

Dockerfile

@@ -5,7 +5,6 @@ COPY . immuneML
 
 RUN DEBIAN_FRONTEND=noninteractive apt-get update
 RUN DEBIAN_FRONTEND=noninteractive apt-get install python3.8 python3-pip git-all -y
-RUN pip3 install setuptools==50.3.2 cython
 
 # install the dependency CompAIRR
 RUN git clone https://github.com/uio-bmi/compairr.git compairr_folder
@@ -14,6 +13,3 @@ 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

docs/source/installation/install_with_package_manager.rst

@@ -65,7 +65,19 @@ see the virtual environment documentation linked above):
 
   source ./immuneml_venv/bin/activate
 
-3. To install `immuneML from PyPI <https://pypi.org/project/immuneML/>`_ in this virtual environment, run the following:
+3. If not already up-to-date, update pip:
+
+.. code-block:: console
+
+  python3 -m pip install --upgrade pip
+
+4. If not already installed, install the wheel package. If it is not installed, the installation of some of the dependencies might default to legacy 'setup.py install'.
+
+.. code-block:: console
+
+  pip install wheel
+
+5. To install `immuneML from PyPI <https://pypi.org/project/immuneML/>`_ in this virtual environment, run the following:
 
 .. code-block:: console
 

immuneML/environment/Constants.py

@@ -1,6 +1,6 @@
 class Constants:
 
-    VERSION = "2.2.1"
+    VERSION = "2.2.2"
 
     # encoding constants
     FEATURE_DELIMITER = "-"

requirements.txt

@@ -1,3 +1,4 @@
+numpy>=1.18.5
 pytest>=4
 pandas>=1
 PyYAML>=5.3
@@ -11,7 +12,6 @@ airr>=1
 fishersapi
 pystache
 torch>=1.5.1
-numpy>=1.18.5
 h5py<=2.10.0
 dill>=0.3
 tqdm>=0.24

setup.py

@@ -20,10 +20,10 @@ def import_requirements(filename) -> list:
     author="immuneML Team",
     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", "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"],
+    install_requires=["numpy>=1.18.5", "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", "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"],
     extras_require={
         "TCRdist": ["parasail==1.2", "tcrdist3>=0.1.6"]
     },