Merge pull request #57 from broadinstitute/dp-bump

update build and dependencies
broadinstitute · Sep 20, 2024 · e5d246c · e5d246c
2 parents 8603105 + 905eea9
commit e5d246c
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Showing 8 changed files with 18 additions and 16 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -8,8 +8,6 @@ on:
   release:
     types:
       - created
-  schedule:
-    - cron: '0 18 * * 1' # weekly at 18:00 on Mondays
 
 env:
   HOME: "${{ github.workspace }}"

diff --git a/Dockerfile b/Dockerfile
@@ -1,11 +1,11 @@
-FROM quay.io/broadinstitute/viral-core:2.3.1
+FROM quay.io/broadinstitute/viral-core:2.3.6
 
 LABEL maintainer "viral-ngs@broadinstitute.org"
 
 ENV VIRAL_PHYLO_PATH=$INSTALL_PATH/viral-phylo
 
 COPY requirements-conda.txt $VIRAL_PHYLO_PATH/
-RUN $VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_PHYLO_PATH/requirements-conda.txt
+RUN $VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_PHYLO_PATH/requirements-conda.txt $VIRAL_NGS_PATH/requirements-conda.txt
 
 # Copy all source code into the base repo
 # (this probably changes all the time, so all downstream build

diff --git a/docs/Makefile b/docs/Makefile
@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = --jobs auto
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build

diff --git a/docs/conf.py b/docs/conf.py
@@ -23,10 +23,11 @@
 
 # -- Mock out the heavyweight pip packages, esp those that require C ----
 import mock
-MOCK_MODULES = ['scipy', 'pysam', 'Bio', 'Bio.AlignIO', 'Bio.Alphabet',
+MOCK_MODULES = ['scipy', 'pysam',
+                'Bio', 'Bio.AlignIO', 'Bio.Alphabet',
                 'Bio.Alphabet.IUPAC', 'Bio.SeqIO', 'Bio.Data.IUPACData',
                 'Bio.Seq', 'Bio.SeqRecord', 'pybedtools', 'pybedtools.BedTool',
-                'arrow', 'zstd', 'bz2']
+                'arrow', 'zstd', 'bz2', 'lz4.frame']
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = mock.Mock()
 
@@ -61,7 +62,7 @@ def _get_viral_core():
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.imgmath', 'sphinxarg.ext',]
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.imgmath', 'sphinxarg.ext', 'sphinx_rtd_theme']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -130,7 +131,7 @@ def _get_viral_core():
 # a list of builtin themes.
 on_rtd = os.environ.get('READTHEDOCS') == 'True'
 if on_rtd:
-    html_theme = 'default'
+    html_theme = 'sphinx_rtd_theme'
 else:
     import sphinx_rtd_theme
     html_theme = "sphinx_rtd_theme"

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,8 +1,8 @@
-jinja2==3.1.2 # https://github.com/readthedocs/readthedocs.org/issues/9037#issuecomment-1077818554
-Sphinx==5.3.0 #override sphinx pinning done by RTD: https://docs.readthedocs.io/en/stable/build-default-versions.html#external-dependencies
-sphinx-argparse
-sphinx-rtd-theme==1.1.1
+jinja2==3.1.4 # https://github.com/readthedocs/readthedocs.org/issues/9037#issuecomment-1077818554
+Sphinx==7.4.7 #override sphinx pinning done by RTD: https://docs.readthedocs.io/en/stable/build-default-versions.html#external-dependencies
+sphinx-argparse==0.5.2
+sphinx-rtd-theme>=2.0.0
 matplotlib>=2.2.4
-PyYAML==6.0
+PyYAML==6.0.1
 mock==5.0.1
 recommonmark
diff --git a/requirements-conda.txt b/requirements-conda.txt
@@ -1,8 +1,9 @@
 bamtools>=2.5.2
+lofreq=2.1.5
 mafft=7.508
 mummer4>=4.0.0rc1
 muscle=3.8.1551
 snpeff=4.3.1t
-tbl2asn-forever>=25.7.1f
+table2asn=1.28.1111
+tbl2asn-forever>=25.7.2f
 vphaser2=2.0
-# Python packages below
diff --git a/test/unit/test_intrahost.py b/test/unit/test_intrahost.py
@@ -152,6 +152,7 @@ def test_single_strand_bias_hard_filter(self):
 
 
 #@unittest.skipIf(tools.is_osx(), "vphaser2 osx binary from bioconda has issues")
+@unittest.skip("vphaser2 behaving unpredictably; not used in WDL pipelines")
 class TestPerSample(test.TestCaseWithTmp):
     ''' This tests step 1 of the iSNV calling process
         (intrahost.vphaser_one_sample), which runs V-Phaser2 on

diff --git a/test/unit/test_tools_vphaser2.py b/test/unit/test_tools_vphaser2.py
@@ -12,6 +12,7 @@
 
 
 #@unittest.skipIf(tools.is_osx(), "vphaser2 osx binary from bioconda has issues")
+@unittest.skip("vphaser2 behaving unpredictably; not used in WDL pipelines")
 class TestVPhaser2(TestCaseWithTmp):
 
     def test_vphaser2(self):