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addressing documentation build failures; testing ReadTheDocs build check for PRs #31

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merged 3 commits into from
Mar 18, 2024
Merged

addressing documentation build failures; testing ReadTheDocs build check for PRs #31

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26bb482
attempt at resolving existing-repo collisions
tomkinsc Mar 28, 2023
7179eca
move subprocess import
tomkinsc Mar 28, 2023
140f3d0
also check for presence of assembly.py before waiving clone of viral-…
tomkinsc Mar 28, 2023
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24 changes: 17 additions & 7 deletions docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@

import sys
import os
import subprocess

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
Expand All @@ -30,25 +31,34 @@
sys.modules[mod_name] = mock.Mock()

# -- Obtain GIT version --
import subprocess


def _git_version():
cmd = ['git', 'describe', '--tags', '--always'] # omit "--dirty" from doc build
out = subprocess.check_output(cmd)
if type(out) != str:
out = out.decode('utf-8')
return out.strip()


__version__ = _git_version()


# -- Obtain upstream viral-core module: this is super hacky and not pinned to any version
def _get_viral_core():
cmd = ['git', 'clone', '--depth=1', 'https://github.com/broadinstitute/viral-core.git']
subprocess.check_call(cmd)
sys.path.insert(0, os.path.dirname(os.path.abspath('viral-core')))
viral_core_dir = os.path.abspath('viral-core')

# if the viral-core dir and its file exist, pull the latest
if os.path.exists(os.path.join(viral_core_dir,"assembly.py")): # ToDo: check if empty instead
cmd = ['git', '-C', viral_core_dir, 'pull', '--depth=1', 'https://github.com/broadinstitute/viral-core.git']
subprocess.check_call(cmd)
# otherwise clone viral-core, removing the viral-core directory if present
else:
if os.path.isdir(viral_core_dir):
os.remove(viral_core_dir, missing_ok=True)
cmd = ['git', 'clone', '--depth=1', 'https://github.com/broadinstitute/viral-core.git']
subprocess.check_call(cmd)

viral_core_parent_dir = os.path.dirname(os.path.abspath('viral-core'))
if viral_core_parent_dir not in sys.path:
sys.path.insert(0, viral_core_parent_dir)
_get_viral_core()


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