From a95e4e19070fe06b67b806f995b209f190a7af9a Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Tue, 26 Mar 2024 13:49:31 -0400
Subject: [PATCH] added extra ensembl install paths

---
 .github/workflows/tests.yml |  3 +-
 .travis.yml                 | 92 -------------------------------------
 2 files changed, 2 insertions(+), 93 deletions(-)
 delete mode 100644 .travis.yml

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index b317d8f..b54d55b 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -47,7 +47,8 @@ jobs:
           echo "Before installing Ensembl releases" && df -h
           pyensembl install --release 75 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh37.75/
           pyensembl install --release 102 --species mouse --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.102/
-          echo "After installing Ensembl releases" && df -h
+          pyensembl install --release 93 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.93/
+          pyensembl install --release 93 --species mouse --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.93/
       - name: Test with pytest
         run: |
           # configure netmhc-bundle paths
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 3ff2cd2..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,92 +0,0 @@
-# Don't use container-based infrastructure, sudo enabled has 18G disk
-# whereas sudo disabled has only 9G
-sudo: true
-language: python
-python:
-  - "3.6"
-  - "3.7"
-git:
-  # don't need the default depth of 50
-  # but don't want to use a depth of 1 since that affects
-  # whether jobs run when you have multiple commits queued
-  # https://github.com/travis-ci/travis-ci/issues/4575
-  depth: 10
-cache:
-  pip: true
-  # cache pip files; directory used for Ensembl downloads of GTF and FASTA files
-  # along with the indexed db of intervals and ID mappings and pickles
-  # of sequence dictionaries; vaxrank directory containing FM index of reference kmers
-  directories:
-    - $HOME/.cache/pyensembl/GRCh37/ensembl75/
-    - $HOME/.cache/pyensembl/GRCh38/ensembl93/
-    - $HOME/.cache/pyensembl/GRCm38/ensembl93/
-  timeout: 300
-before_install:
-  - 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:$PATH"
-  # reset the shell's lookup table for program name to path mappings
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-  # Useful for debugging any issues with conda
-  - conda info -a
-  # install netmhcbundle
-  - git clone https://mhcbundle:$MHC_BUNDLE_PASS@github.com/openvax/netmhc-bundle.git
-  - export NETMHC_BUNDLE_HOME=$PWD/netmhc-bundle
-  - mkdir tmp
-  - export NETMHC_BUNDLE_TMPDIR=$PWD/tmp
-  - export PATH=$PATH:$NETMHC_BUNDLE_HOME/bin
-  # tells vaxrank where to install the reference peptide cache
-  - export VAXRANK_REF_PEPTIDES_DIR=$HOME/.cache/vaxrank
-env:
-  global:
-    # MHC_BUNDLE_PASS
-    - secure: "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"
-    - KERAS_BACKEND=tensorflow
-addons:
-  apt:
-    packages:
-    # Needed for NetMHC
-    - tcsh
-install:
-  - >
-      conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION
-      numpy nose pylint cython tensorflow tensorboard
-  - source activate test-environment
-  # install pysam from conda because I'm having trouble installing Cython
-  # for Python 3 on Travis
-  - conda install -c bioconda pysam
-  - pip install -r requirements.txt
-  - pip install .
-  - pip install coveralls
-before_script:
-  - ./lint.sh
-  - >
-      pyensembl install
-      --release 75
-      --species human
-      --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh37.75/
-  - >
-      pyensembl install
-      --release 93
-      --species human
-      --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.93/
-  - >
-      pyensembl install
-      --release 93
-      --species mouse
-      --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.93/
-script:
-  - travis_wait nosetests -sv test -a '!skip' --with-coverage --cover-package=vaxrank
-after_success:
-  coveralls
-deploy:
-  provider: pypi
-  distributions: sdist
-  user: openvax
-  password: # See http://docs.travis-ci.com/user/encryption-keys/
-    secure: "kt07TyCxiumbu2SGZvl7J5LLzsLq0zxcCceOSGb4RE0tFOmiUmDv5LfGKME5lEFhPxleChaq/AILDOudEZO3H9xJY90/dXPgyXJOd6pCOzKq3zIKEjz3MEx3wBizcjR7ucHxYxDQzIBEBeoC4wTIc53mBR5gMgqyG8Dbciueg9Yo5qZED9rq/uY1ELxW2iQsS9LBK7n/blTPTisdmdG3g64eVEDsZD/0egPdupWhlkNuUQlA4LVr2KUifGrtXPL0A/m3CUEABJWre7PJ6motFS1KramP7/PQJwpXmZEHI1ayknNeN2ndMp4Ni64cEhtF/JIRYWBuGxzZXSuIv1g8XxKijm/qxSc4Gv0yIiP/Q3pZ5hfSC1RZhcpkc3ugCSOy5VwlF5O0P/EflMnsUE9ZRFON3s5+yjsJtNldsCRpdEsquFPn0BJC4kOdWKfIkYuhln6xcJawl+8uKlCJuOa1vZcsJ16E6RPN3TpkfChaMVBrD6zEbYZfrI5QCMV/uwkwutgV4H95FR0TlnDrOTwAMamxFBN7R8+YEHff9n21c4i7vzjBVlI16W/t2qqmaG/0w1hBhAiYvvV5BLh84km5gSewcjcKjBHVhYscF1Xxyq0CPmKdcOB6ePFbIWh/+NHQzDpzY8yKp9kzkZizZJGUAxsI2ZH3++BzQwcSUn664VY="
-  on:
-    branch: master
-    condition: $TRAVIS_PYTHON_VERSION = "3.6"