From 075c2b75f96093b1dfcc245549f3eca4525dc1a4 Mon Sep 17 00:00:00 2001 From: pavlovicmilena Date: Sun, 8 May 2022 17:42:43 +0200 Subject: [PATCH] fix installation & update version --- Dockerfile | 4 ---- .../installation/install_with_package_manager.rst | 14 +++++++++++++- immuneML/environment/Constants.py | 2 +- requirements.txt | 2 +- setup.py | 8 ++++---- 5 files changed, 19 insertions(+), 11 deletions(-) diff --git a/Dockerfile b/Dockerfile index cb495eaf7..3b1157bc8 100644 --- a/Dockerfile +++ b/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 diff --git a/docs/source/installation/install_with_package_manager.rst b/docs/source/installation/install_with_package_manager.rst index 0258be83a..5236595e3 100644 --- a/docs/source/installation/install_with_package_manager.rst +++ b/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 `_ 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 `_ in this virtual environment, run the following: .. code-block:: console diff --git a/immuneML/environment/Constants.py b/immuneML/environment/Constants.py index 52a7e91d0..98815a643 100644 --- a/immuneML/environment/Constants.py +++ b/immuneML/environment/Constants.py @@ -1,6 +1,6 @@ class Constants: - VERSION = "2.2.1" + VERSION = "2.2.2" # encoding constants FEATURE_DELIMITER = "-" diff --git a/requirements.txt b/requirements.txt index b4fa0e0f6..208dd8ea5 100644 --- a/requirements.txt +++ b/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 diff --git a/setup.py b/setup.py index 2a74e115f..e91054907 100644 --- a/setup.py +++ b/setup.py @@ -20,10 +20,10 @@ def import_requirements(filename) -> list: author="immuneML Team", author_email="milenpa@student.matnat.uio.no", 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"] },