Merge pull request #255 from debbiemarkslab/develop

Finalize for new release (v0.1.0)

.github/workflows/build_and_test.yml

@@ -0,0 +1,42 @@
+name: build_and_test
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [3.6]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install and configure conda
+      run: |
+        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+        bash miniconda.sh -b -p $HOME/miniconda
+        export PATH="$HOME/miniconda/bin:$PATH"
+        hash -r
+        conda config --set always_yes yes --set changeps1 no
+        conda update -q conda
+        conda info -a
+        conda create -q -n test-environment python=${{ matrix.python-version }} numpy scipy numba pandas matplotlib
+        source activate test-environment
+    - name: Run setup.py
+      run: |
+        python setup.py sdist --formats=zip -k
+        find ./dist -iname "*.zip" -print0 | xargs -0 pip install
+        pip install codecov
+    - name: Download test files
+      run: |
+        wget https://marks.hms.harvard.edu/evcouplings_test_cases/data/evcouplings_test_cases.tar.gz
+        tar -xf evcouplings_test_cases.tar.gz -C $HOME/
+    - name: Run tests in headless xvfb environment
+      uses: GabrielBB/xvfb-action@v1
+      with:
+        run: coverage run -m unittest discover -s test -p "Test*.py"

.github/workflows/build_test_and_push.yml

@@ -0,0 +1,54 @@
+name: build_test_and_push
+
+on:
+  release:
+    types: [released]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install and configure conda
+      run: |
+        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+        bash miniconda.sh -b -p $HOME/miniconda
+        export PATH="$HOME/miniconda/bin:$PATH"
+        hash -r
+        conda config --set always_yes yes --set changeps1 no
+        conda update -q conda
+        conda info -a
+        conda create -q -n test-environment python=${{ matrix.python-version }} numpy scipy numba pandas matplotlib
+        source activate test-environment
+    - name: Run setup.py
+      run: |
+        python setup.py sdist --formats=zip -k
+        find ./dist -iname "*.zip" -print0 | xargs -0 pip install
+        pip install codecov
+    - name: Download test files
+      run: |
+        wget https://marks.hms.harvard.edu/evcouplings_test_cases/data/evcouplings_test_cases.tar.gz
+        tar -xf evcouplings_test_cases.tar.gz -C $HOME/
+    - name: Run tests in headless xvfb environment
+      uses: GabrielBB/xvfb-action@v1
+      with:
+        run: coverage run -m unittest discover -s test -p "Test*.py"
+    - name: Publish evcouplings to test PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.PYPI_ACCESS_TOKEN_TEST }}
+        repository_url: https://test.pypi.org/legacy/
+    - name: Publish evcouplings to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.PYPI_ACCESS_TOKEN }}

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/debbiemarkslab/EVcouplings.svg?branch=master)](https://travis-ci.org/debbiemarkslab/EVcouplings)
+[![build_and_test Actions Status](https://github.com/debbiemarkslab/EVcouplings/workflows/build_and_test/badge.svg?branch=master)](https://github.com/debbiemarkslab/EVcouplings/actions) [![PyPI version](https://badge.fury.io/py/evcouplings.svg)](https://badge.fury.io/py/evcouplings)
 # EVcouplings
 
 Predict protein structure, function and mutations using evolutionary sequence covariation.
@@ -15,18 +15,19 @@ EVcouplings requires a Python >= 3.5 installation. Since it depends on some pack
 
 #### Installation
 
-To install the latest version of EVcouplings, *currently please do not use the outdated PyPI release (i.e. do not pip install evcouplings)*. Instead, run
+To install the latest version of EVcouplings on PyPI,
 
-    pip install https://github.com/debbiemarkslab/EVcouplings/archive/develop.zip
+    pip install evcouplings
 
-To obtain the latest version of EVcouplings from the github repository, run
+To obtain the latest development version of EVcouplings from the github repository, run
 
-    pip install git+https://github.com/debbiemarkslab/EVcouplings.git
+    pip install https://github.com/debbiemarkslab/EVcouplings/archive/develop.zip
 
 and to update to the latest version after previously installing EVcouplings from the repository, run
 
-    pip install -U --no-deps git+https://github.com/debbiemarkslab/EVcouplings.git
+    pip install -U --no-deps https://github.com/debbiemarkslab/EVcouplings/archive/develop.zip
 
+Installation will take seconds.
 
 ### External software tools
 
@@ -69,7 +70,7 @@ Download and install [PSIPRED](http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred
 
 evcouplings uses maxcluster to compare predicted 3D structure models to experimental protein structures, if there are any for the target protein or one
 of its homologs. Installation is only required if you want to run the *fold* stage of the computational pipeline.
- 
+
 Download [maxcluster](http://www.sbg.bio.ic.ac.uk/~maxcluster/) and place it in a directory of your choice.
 
 ### Databases
@@ -86,17 +87,17 @@ Please see
 
     evcouplings_dbupdate --help
 
-for how to download the respective databases. Note that this may take a while, especially the generation of post-processed SIFTS mapping files. 
+for how to download the respective databases. Note that this may take a while, especially the generation of post-processed SIFTS mapping files.
 
 #### Sequence databases for EVcomplex
 Running the EVcouplings pipeline for protein complexes (aka EVcomplex) requires two pre-computed databases. You can download these databases here:
 
 ena_genome_location_table: https://marks.hms.harvard.edu/evcomplex_databases/cds_pro_2017_02.txt
 uniprot_to_embl_table: https://marks.hms.harvard.edu/evcomplex_databases/idmapping_uniprot_embl_2017_02.txt
 
-Save these databases in your local environment, and then add the paths to the local copies of these databases to your config file for the complex pipeline. 
+Save these databases in your local environment, and then add the paths to the local copies of these databases to your config file for the complex pipeline.
 
-In future releases these databases will be generated automatically. 
+In future releases these databases will be generated automatically.
 
 #### Other sequence databases
 
@@ -107,7 +108,7 @@ You can however use any sequence database of your choice in FASTA format if you
 Relevant PDB structures for comparison of ECs and 3D structure predictions will be automatically fetched from the web in the new compressed MMTF format on a per-job basis. You can however also pre-download the entire PDB and place the structures in a directory if you want to (and set pdb_mmtf_dir in your job configuration).
 
 Uniprot to PDB index mapping files will be automatically generated by EVcouplings based on the SIFTS database.
-You can either generate the files by running *evcouplings_dbupdate* (see above, preferred), or by pointing the sifts_mapping_table and sifts_sequence_db configuration parameters to file paths inside an already existing directory. If these files do not yet exist, they will be created by fetching and integrating data from the web (this may take a while) when the pipeline is first run and saved under the given file paths. 
+You can either generate the files by running *evcouplings_dbupdate* (see above, preferred), or by pointing the sifts_mapping_table and sifts_sequence_db configuration parameters to file paths inside an already existing directory. If these files do not yet exist, they will be created by fetching and integrating data from the web (this may take a while) when the pipeline is first run and saved under the given file paths.
 
 ## Documentation and tutorials
 
@@ -140,16 +141,19 @@ Hopf, T. A., Schärfe, C. P. I., Rodrigues, J. P. G. L. M., Green, A. G., Kohlba
 
 Hopf, T. A., Ingraham, J. B., Poelwijk, F.J., Schärfe, C.P.I., Springer, M., Sander, C., & Marks, D. S. (2017). Mutation effects predicted from sequence co-variation. *Nature Biotechnology* **35**, 128–135 doi:10.1038/nbt.3769
 
+Green, A. G. and Elhabashy, H., Brock, K. P., Maddamsetti, R., Kohlbacher, O., Marks, D. S. (2019) Proteom-scale discovery of protein interactions with residue-level resolution using sequence coevolution. BioRxiv (in review). https://doi.org/10.1101/791293
+
 ## Contributors
 
 EVcouplings is developed in the labs of [Debora Marks](http://marks.hms.harvard.edu) and [Chris Sander](http://sanderlab.org/) at Harvard Medical School.
 
 * [Thomas Hopf](mailto:thomas.hopf@gmail.com) (development lead)
-* Anna Green
+* Anna G. Green
 * Benjamin Schubert
 * Sophia Mersmann
 * Charlotta Schärfe
 * Agnes Toth-Petroczy
 * John Ingraham
 * Rob Sheridan
 * Christian Dallago
+* Joe Min

setup.py

@@ -22,6 +22,7 @@
 
     description='A Framework for evolutionary couplings analysis',
     long_description=readme,
+    long_description_content_type='text/markdown',
 
     # The project's main homepage.
     url='https://github.com/debbiemarkslab/EVcouplings',

test/TestComplex.py

@@ -18,7 +18,8 @@
 from evcouplings.complex.protocol import *
 from evcouplings.align import Alignment
 
-TRAVIS_PATH = "/home/travis/evcouplings_test_cases/complex_test"
+TRAVIS_PATH = os.getenv('HOME') + "/evcouplings_test_cases/complex_test"
+# TRAVIS_PATH = "/home/travis/evcouplings_test_cases/complex_test"
 # TRAVIS_PATH = "/Users/AG/Dropbox/evcouplings_dev/test_cases/for_B/complex_test"
 
 class TestComplex(TestCase):

test/TestFold.py

@@ -15,7 +15,8 @@
 from evcouplings.fold import haddock_dist_restraint
 from evcouplings.fold.protocol import complex_dock
 
-TRAVIS_PATH = "/home/travis/evcouplings_test_cases"
+TRAVIS_PATH = os.getenv('HOME') + "/evcouplings_test_cases"
+# TRAVIS_PATH = "/home/travis/evcouplings_test_cases"
 #TRAVIS_PATH = "/Users/AG/Dropbox/evcouplings_dev/test_cases/for_B"
 COMPLEX_PATH = "{}/complex_test".format(TRAVIS_PATH)
 

test/TestMutation.py

@@ -17,7 +17,8 @@
 from evcouplings.mutate.protocol import *
 from evcouplings.couplings.model import CouplingsModel
 
-TRAVIS_PATH = "/home/travis/evcouplings_test_cases"
+TRAVIS_PATH = os.getenv('HOME') + "/evcouplings_test_cases"
+# TRAVIS_PATH = "/home/travis/evcouplings_test_cases"
 #TRAVIS_PATH = "/Users/AG/Dropbox/evcouplings_dev/test_cases/for_B"
 MONOMER_PATH = "{}/monomer_test".format(TRAVIS_PATH)
 COMPLEX_PATH = "{}/complex_test".format(TRAVIS_PATH)

test/TestUtilsCalculate.py

@@ -4,7 +4,8 @@
 from evcouplings.couplings import CouplingsModel
 import numpy as np
 
-MONO_MODEL = "/home/travis/evcouplings_test_cases/monomer_test/couplings/RASH_HUMAN_b03.model"
+MONO_MODEL = os.getenv('HOME') + "/evcouplings_test_cases/monomer_test/couplings/RASH_HUMAN_b03.model"
+# MONO_MODEL = "/home/travis/evcouplings_test_cases/monomer_test/couplings/RASH_HUMAN_b03.model"
 
 
 class TestUtilsHelpers(TestCase):