Small fixes to get travis to pass...

.travis.yml

@@ -29,6 +29,7 @@ install:
   - conda config --add channels conda-forge
   - conda config --add channels omnia
   - conda config --add channels bioconda
+  - conda config --add channels salilab
   - conda info -a
   # Install packages
   - conda update -q conda
@@ -40,16 +41,8 @@ before_script:
   - source activate _test
   - conda install -q --yes fake_provean fake_foldx anaconda-client
 script:
-  - |
-    if [[ $TEST_SUITE != 'test_unittests' ]] ; then
-        source "${SCRIPTS_DIR}/configure_tests.sh"
-        cd "${TEST_DIR}"
-        ls
-        travis_wait 119 "${SCRIPTS_DIR}/${TEST_SUITE}.sh"
-    else
-        py.test
-        "${SCRIPTS_DIR}/build-docs.sh"
-    fi
+  # Run tests
+  - travis_wait 119 "${SCRIPTS_DIR}/travis-ci.sh"
 after_success:
   - echo "Success!"
   - pip install codecov

devtools/conda-recipe/meta.yaml

@@ -16,12 +16,22 @@ requirements:
     - python
     - pyyaml
     - requests
+    - psutil
+    - retrying
+    - fastcache
     # Scientific python
     - numpy
     - scipy
     - pandas
     - scikit-learn
     - biopython
+    - libfaketime
+    - modeller
+    # Database access
+    - sqlalchemy
+    - sqlite
+    - mysqlclient
+    - psycopg2
   run:
     # Basic python
     - python
@@ -36,6 +46,8 @@ requirements:
     - pandas
     - scikit-learn
     - biopython
+    - libfaketime
+    - modeller
     # Database access
     - sqlalchemy
     - sqlite
@@ -49,11 +61,9 @@ requirements:
     - pops
     - msms
     - t_coffee
-    - modeller
     - cd-hit
     # - provean  # can't install fake_provean for tests if this is installed...
     # - foldx  # private only and breaks readthedocs
-    - libfaketime
 
 test:
   requires:

devtools/travis-ci/build-docs.sh

@@ -11,11 +11,9 @@ cd "${TRAVIS_BUILD_DIR}/docs"
 GITHUB_USERNAME=$(dirname $TRAVIS_REPO_SLUG)
 GITHUB_REPONAME=$(basename $TRAVIS_REPO_SLUG)
 
-# Install sphinx requirements
-pip install -U pip
-# Work around missing dependency in conda.
+conda install sphinx
 pip install auxlib
-pip install -r requirements.txt
+pip install sphinxcontrib-programoutput
 
 # Build the documentation
 mkdir -p _build_gh_pages

devtools/travis-ci/configure_tests.sh

@@ -18,7 +18,8 @@ fi
 
 # Copy package data
 mkdir -p "${TEST_DIR}"
-rsync -av "${SRC_DIR}" "${TEST_DIR}" --exclude='[._]*'
+rsync -av "${SRC_DIR}/tests/" "${TEST_DIR}" --exclude='[._]*'
+ls ${TEST_DIR}
 
 
 # Common directories
@@ -33,5 +34,5 @@ touch "${BLAST_DB_DIR}/pdbaa.pal"
 
 # ====== Database ======
 if [[ -z ${TEST_SUITE} || ${TEST_SUITE} == database* ]] ; then
-    ${SCRIPTS_DIR}/configure_database.sh
+    source ${SCRIPTS_DIR}/configure_database.sh
 fi

devtools/travis-ci/test_database_pipeline_1.sh

@@ -16,7 +16,7 @@ ARCHIVE_DIR="${TEST_DIR}/archive"
 mkdir -p "${ARCHIVE_DIR}"
 
 # Update the configuration file
-cp -f "${SCRIPTS_DIR}/database_pipeline.ini" "${CONFIG_FILE}"
+cp -f "${TEST_DIR}/database_pipeline.ini" "${CONFIG_FILE}"
 sed -i "s|^pdb_dir = .*|pdb_dir = ${PDB_DIR}|" "${CONFIG_FILE}"
 sed -i "s|^blast_db_dir = .*|blast_db_dir = ${BLAST_DB_DIR}|" "${CONFIG_FILE}"
 sed -i "s|^archive_dir = .*|archive_dir = ${ARCHIVE_DIR}|" "${CONFIG_FILE}"
@@ -28,5 +28,5 @@ sed -i "s|^archive_type = .*|archive_type = directory|" "${CONFIG_FILE}"
 7z -bd x "${TEST_DIR}/elaspic.kimlab.org/uniprot_domain_pair/uniprot_domain_pair.7z" -o"${ARCHIVE_DIR}"
 
 # Run tests
-py.test "${TEST_DIR}/tests/test_database_pipeline.py" -vsx --cache-clear --cov=elaspic \
+py.test "${TEST_DIR}/test_database_pipeline.py" -vsx --cache-clear --cov=elaspic \
     --config-file="${CONFIG_FILE}"

devtools/travis-ci/test_database_pipeline_2.sh

@@ -23,5 +23,5 @@ sed -i "s|^archive_dir = .*|archive_dir = ${ARCHIVE_DIR}|" "${CONFIG_FILE}"
 sed -i "s|^archive_type = .*|archive_type = 7zip|" "${CONFIG_FILE}"
 
 # Run tests
-py.test "${TEST_DIR}/tests/test_database_pipeline.py" -vsx --cache-clear --cov=elaspic \
+py.test "${TEST_DIR}/test_database_pipeline.py" -vsx --cache-clear --cov=elaspic \
     --config-file="${CONFIG_FILE}"

devtools/travis-ci/travis-ci.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -ev
+
+# Sanity checks
+if [[ -z ${TEST_SUITE} || \
+      -z ${SCRIPTS_DIR} || \
+      -z ${TEST_DIR} ]] ; then
+    echo 'Required environment variable not set!'
+    exit
+fi
+
+if [[ ${TEST_SUITE} = 'test_unittests' ]] ; then
+    py.test
+    "${SCRIPTS_DIR}/build-docs.sh"
+else
+    source "${SCRIPTS_DIR}/configure_tests.sh"
+    cd "${TEST_DIR}"
+    ls
+    "${SCRIPTS_DIR}/${TEST_SUITE}.sh"
+fi

setup.cfg

@@ -1,16 +1,16 @@
-[aliases]
-test=pytest
-
 [bumpversion]
-files = conda/elaspic/meta.yaml setup.py
+files = devtools/conda-recipe/meta.yaml setup.py docs/conf.py
 commit = False
 tag = True
 message = "Release {new_version}"
 current_version = 1.0.22
 
+[aliases]
+test = pytest
+
 [pytest]
-addopts = -sv --cov=elaspic
-python_files = tests/test_helper.py tests/test_pep8.py
+addopts = -sv --cov=elaspic --ignore=setup.py
+python_files = tests/test_helper.py tests/test_pep8.py tests/test_structure_analysis.py
 
 [flake8]
 ignore = D100,D101,D102,D103,E402

setup.py

@@ -1,5 +1,5 @@
 import os.path as op
-from setuptools import setup, find_packages, Command
+from setuptools import setup, Command
 import yaml
 
 
@@ -37,7 +37,7 @@ def finalize_options(self):
     url=META.get('about', {}).get('home', ''),
     author='kimlab',
     author_email='alex.strokach@utoronto.ca',
-    packages=find_packages('elaspic'),
+    packages=['elaspic'],
     package_data={'elaspic': ['data/*']},
     long_description=read("README.md"),
     entry_points={'console_scripts': META.get('build', {}).get('entry_points', '')},

tests/conftest.py

@@ -8,7 +8,6 @@
     TESTS_BASE_DIR = op.dirname(__file__)
 except NameError:
     TESTS_BASE_DIR = os.getcwd()
-assert op.split(TESTS_BASE_DIR)[-1] == 'tests'
 
 TESTS_DATA_DIR = op.join(TESTS_BASE_DIR, 'data')