Merge pull request #45 from LadnerLab/autopepsirf-ISS26

Autopepsirf iss26

Author: Num0Programmer

q2_ps_plot/__init__.py

@@ -1,12 +1,16 @@
 #!/usr/bin/env python
-from q2_ps_plot.actions.zenrich import zenrich
-from q2_ps_plot.actions.zenrich_tsv import zenrich_tsv
-from q2_ps_plot.actions.boxplot import readCountsBoxplot
-from q2_ps_plot.actions.scatter import repScatters
+from . import _version
+
+__all__ = [
+    "zenrich", "zenrich_tsv", "readCountsBoxplot",
+    "repScatters", "enrichmentRCBoxplot", "proteinHeatmap"
+]
+__version__ = _version.get_versions()["version"]
+
 from q2_ps_plot.actions.boxplot import enrichmentRCBoxplot
+from q2_ps_plot.actions.boxplot import readCountsBoxplot
 from q2_ps_plot.actions.heatmap import proteinHeatmap
+from q2_ps_plot.actions.scatter import repScatters
+from q2_ps_plot.actions.zenrich import zenrich
+from q2_ps_plot.actions.zenrich_tsv import zenrich_tsv
 
-__all__ = ['zenrich', 'zenrich_tsv', 'readCountsBoxplot', 'repScatters', 'enrichmentRCBoxplot', 'proteinHeatmap']
-
-from . import _version
-__version__ = _version.get_versions()['version']

q2_ps_plot/_version.py

@@ -1,4 +1,3 @@
-
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -77,10 +76,13 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
         try:
             dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
-                                       stdout=subprocess.PIPE,
-                                       stderr=(subprocess.PIPE if hide_stderr
-                                               else None))
+            process = subprocess.Popen(
+                [command] + args,
+                cwd=cwd,
+                env=env,
+                stdout=subprocess.PIPE,
+                stderr=(subprocess.PIPE if hide_stderr else None)
+            )
             break
         except EnvironmentError:
             e = sys.exc_info()[1]
@@ -115,15 +117,21 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {"version": dirname[len(parentdir_prefix):],
-                    "full-revisionid": None,
-                    "dirty": False, "error": None, "date": None}
+            return {
+                "version": dirname[len(parentdir_prefix):],
+                "full-revisionid": None,
+                "dirty": False,
+                "error": None,
+                "date": None
+            }
         rootdirs.append(root)
         root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print("Tried directories %s but none started with prefix %s" %
-              (str(rootdirs), parentdir_prefix))
+        print(
+            "Tried directories %s but none started with prefix %s"
+            % (str(rootdirs), parentdir_prefix)
+        )
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
@@ -162,7 +170,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         raise NotThisMethod("Short version file found")
     date = keywords.get("date")
     if date is not None:
-        # Use only the last line.  Previous lines may contain GPG signature
+        # Use only the last line. Previous lines may contain GPG signature
         # information.
         date = date.splitlines()[-1]
 
@@ -207,16 +215,23 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
                 continue
             if verbose:
                 print("picking %s" % r)
-            return {"version": r,
-                    "full-revisionid": keywords["full"].strip(),
-                    "dirty": False, "error": None,
-                    "date": date}
+            return {
+                "version": r,
+                "full-revisionid": keywords["full"].strip(),
+                "dirty": False,
+                "error": None,
+                "date": date
+            }
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {"version": "0+unknown",
-            "full-revisionid": keywords["full"].strip(),
-            "dirty": False, "error": "no suitable tags", "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": keywords["full"].strip(),
+        "dirty": False,
+        "error": "no suitable tags",
+        "date": None
+    }
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
@@ -231,19 +246,24 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
 
-    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                   hide_stderr=True)
+    _, rc = runner(
+        GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True
+    )
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
         raise NotThisMethod("'git rev-parse --git-dir' returned error")
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = runner(GITS, ["describe", "--tags", "--dirty",
-                                     "--always", "--long",
-                                     "--match", "%s*" % tag_prefix],
-                              cwd=root)
+    describe_out, rc = runner(
+        GITS,
+        ["describe", "--tags", "--dirty",
+         "--always", "--long", "--match",
+         "%s*" % tag_prefix
+         ],
+        cwd=root
+    )
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
@@ -258,8 +278,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
 
-    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
-                             cwd=root)
+    branch_name, rc = runner(
+        GITS, ["rev-parse", "--abbrev-ref", "HEAD"], cwd=root
+    )
     # --abbrev-ref was added in git-1.6.3
     if rc != 0 or branch_name is None:
         raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
@@ -308,8 +329,10 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
         mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
             # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = ("unable to parse git-describe output: '%s'"
-                               % describe_out)
+            pieces["error"] = (
+                "unable to parse git-describe output: '%s'"
+                % describe_out
+            )
             return pieces
 
         # tag
@@ -318,8 +341,10 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
-                               % (full_tag, tag_prefix))
+            pieces["error"] = (
+                "tag '%s' doesn't start with prefix '%s'"
+                % (full_tag, tag_prefix)
+            )
             return pieces
         pieces["closest-tag"] = full_tag[len(tag_prefix):]
 
@@ -336,7 +361,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
         pieces["distance"] = int(count_out)  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
+    date = runner(
+        GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root
+    )[0].strip()
     # Use only the last line.  Previous lines may contain GPG signature
     # information.
     date = date.splitlines()[-1]
@@ -370,8 +397,7 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -400,8 +426,7 @@ def render_pep440_branch(pieces):
         rendered = "0"
         if pieces["branch"] != "master":
             rendered += ".dev0"
-        rendered += "+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
+        rendered += "+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -544,11 +569,13 @@ def render_git_describe_long(pieces):
 def render(pieces, style):
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {"version": "unknown",
-                "full-revisionid": pieces.get("long"),
-                "dirty": None,
-                "error": pieces["error"],
-                "date": None}
+        return {
+            "version": "unknown",
+            "full-revisionid": pieces.get("long"),
+            "dirty": None,
+            "error": pieces["error"],
+            "date": None
+        }
 
     if not style or style == "default":
         style = "pep440"  # the default
@@ -572,9 +599,13 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {"version": rendered, "full-revisionid": pieces["long"],
-            "dirty": pieces["dirty"], "error": None,
-            "date": pieces.get("date")}
+    return {
+        "version": rendered,
+        "full-revisionid": pieces["long"],
+        "dirty": pieces["dirty"],
+        "error": None,
+        "date": pieces.get("date")
+    }
 
 
 def get_versions():
@@ -588,8 +619,9 @@ def get_versions():
     verbose = cfg.verbose
 
     try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
-                                          verbose)
+        return git_versions_from_keywords(
+            get_keywords(), cfg.tag_prefix, verbose
+        )
     except NotThisMethod:
         pass
 
@@ -601,10 +633,13 @@ def get_versions():
         for _ in cfg.versionfile_source.split('/'):
             root = os.path.dirname(root)
     except NameError:
-        return {"version": "0+unknown", "full-revisionid": None,
-                "dirty": None,
-                "error": "unable to find root of source tree",
-                "date": None}
+        return {
+            "version": "0+unknown",
+            "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to find root of source tree",
+            "date": None
+        }
 
     try:
         pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
@@ -618,6 +653,11 @@ def get_versions():
     except NotThisMethod:
         pass
 
-    return {"version": "0+unknown", "full-revisionid": None,
-            "dirty": None,
-            "error": "unable to compute version", "date": None}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": None,
+        "dirty": None,
+        "error": "unable to compute version",
+        "date": None
+    }
+

q2_ps_plot/actions/__init__.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python
+
+__all__ = ["zenrich", "zenrich_tsv"]
+
 from q2_ps_plot.actions.zenrich import zenrich
 from q2_ps_plot.actions.zenrich_tsv import zenrich_tsv
 
-__all__ = ['zenrich', 'zenrich_tsv']