1212import logging
1313import hashlib
1414from pathlib import Path
15- from distutils import filelist , log
15+ from distutils import filelist
16+
17+ # Determine default staging area, used in help
18+ default_staging = "/tmp/{0}-lcdb-wf-staging" .format (os .getenv ('USER' ))
19+
20+ usage = f"""
21+ This script assists in the deployment of relevant code from the lcdb-wf
22+ repository to a new deployment directory for running an analysis. It is
23+ intended to be run in a standalone fashion such that with just the script you
24+ can download and deploy a specified version of the workflows.
25+
26+ For example, the following command will clone the GitHub repo to { default_staging }
27+ check out the v9.999 branch, copy the files needed for RNA-seq over to the
28+ "my_analysis_dir" directory, store a read-only file .lcdb-wf-deployment.yaml
29+ with the metadata of the repo used for cloning, and build the conda
30+ environments within "my_analysis_dir":
31+
32+ ./deploy.py \\
33+ --clone \\
34+ --dest my_analysis_dir \\
35+ --flavor rnaseq \\
36+ --build-envs \\
37+ --branch v9.999
38+
39+ Compared to directly cloning the repo, this results in a cleaner deployment
40+ directory that does not have various test infrastructure or workflows not
41+ relevant to the project.
42+ """
1643
1744logging .basicConfig (
1845 format = "%(asctime)s [%(module)s] %(message)s" ,
3158RESET = "\x1b [0m"
3259
3360
34- # Determine default staging area
35- default_staging = "/tmp/{0}-lcdb-wf-staging" .format (os .getenv ('USER' ))
36-
37-
3861def debug (s ):
3962 logging .debug (GRAY + s + RESET )
4063
@@ -51,28 +74,11 @@ def error(s):
5174 logging .error (RED + s + RESET )
5275
5376
77+ def write_include_file (source , flavor = 'all' ):
5478
55- usage = f"""
56- This script assists in the deployment of relevant code from the lcdb-wf
57- repository to a new deployment directory for running an analysis.
58-
59- For example, the following command will clone the GitHub repo to { default_staging }
60- check out the v9.999 branch, copy the files needed for RNA-seq over to the
61- "my_analysis_dir" directory, store a read-only file .lcdb-wf-deployment.yaml
62- with the metadata of the repo used for cloning, and build the conda
63- environments within "my_analysis_dir":
64-
65- ./deploy.py \\
66- --clone \\
67- --dest my_analysis_dir \\
68- --flavor rnaseq \\
69- --build-envs \\
70- --branch v9.999
71-
72- """
73-
74-
75- def write_include_file (flavor = None ):
79+ # Patterns follow that of MANIFEST.in
80+ # (https://packaging.python.org/en/latest/guides/using-manifest-in/),
81+ # and distutils.filelist is used below to parse them.
7682
7783 PATTERN_DICT = {
7884 'rnaseq' : [
@@ -107,17 +113,14 @@ def write_include_file(flavor=None):
107113 }
108114
109115 patterns = []
110- if flavor is None or 'rnaseq' :
116+ if flavor in ( 'full' , 'rnaseq' ) :
111117 patterns .extend (PATTERN_DICT ['rnaseq' ])
112- if flavor is None or 'chipseq' :
118+ if flavor in ( 'full' , 'chipseq' ) :
113119 patterns .extend (PATTERN_DICT ['chipseq' ])
114- if flavor is None or 'full' :
120+ if flavor == 'full' :
115121 patterns .extend (PATTERN_DICT ['full' ])
116122 patterns .extend (PATTERN_DICT ['all' ])
117123
118- HERE = Path (__file__ ).resolve ().parent
119- os .chdir (HERE )
120-
121124 def fastwalk (path ):
122125 """
123126 Find all files recursively, but short-circuit if we get to a conda env to
@@ -134,7 +137,7 @@ def fastwalk(path):
134137 yield os .path .join (root , f ).replace (path + '/' , '' )
135138
136139 f = filelist .FileList ()
137- f .allfiles = list (fastwalk (str ( HERE ) ))
140+ f .allfiles = list (fastwalk (source ))
138141 for pattern in patterns :
139142 f .process_template_line (pattern )
140143 f .sort ()
@@ -144,7 +147,7 @@ def fastwalk(path):
144147 sp .check_output (
145148 ["git" , "ls-tree" , "-r" , "HEAD" , "--name-only" ],
146149 universal_newlines = True ,
147- cwd = str ( HERE ) ,
150+ cwd = source ,
148151 ).splitlines (False ),
149152 )
150153
@@ -153,6 +156,7 @@ def fastwalk(path):
153156 with open (include , 'w' ) as fout :
154157 fout .write ('\n \n ' )
155158 fout .write ('\n ' .join (to_transfer ))
159+
156160 return include
157161
158162
@@ -341,7 +345,6 @@ def build_envs(dest, conda_frontend="mamba"):
341345
342346 ap .add_argument (
343347 "--staging" ,
344- default = default_staging ,
345348 help = """Only used when --clone is specified. Clone the main git repo to
346349 this directory and do a diff on the deploy.py script found there to
347350 ensure this one is up-to-date, and if so then proceed using the new clone as the source.
@@ -384,12 +387,14 @@ def build_envs(dest, conda_frontend="mamba"):
384387 print ("ERROR: --staging was specified but --clone was not. Did you want to use --clone?" , file = sys .stderr )
385388 sys .exit (1 )
386389 if args .clone :
387- source = args .staging
390+ if args .staging is None :
391+ args .staging = default_staging
392+ source = os .path .abspath (args .staging )
388393 clone_repo (args .staging , args .branch , mismatch_ok = args .mismatch_ok )
389394 else :
390395 source = Path (__file__ ).parent .resolve ()
391396
392- include = write_include_file (source )
397+ include = write_include_file (source , flavor )
393398 rsync (include , source , dest , args .rsync_args )
394399 deployment_json (source , dest )
395400
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