Merge pull request #259 from ZELLMECHANIK-DRESDEN/develop

0.9.7

CHANGELOG

@@ -1,3 +1,8 @@
+0.9.7
+ - fix: batch statistical analysis used one measurement per folder (#252)
+ - fix: redrawing-issues of control panels (#253)
+ - docs: minor update
+ - setup: bump dclab from 0.14.7 to 0.18.0
 0.9.6
  - enh: improved support for tdms data (dclab 0.12.0 -> 0.14.7) (e.g. #249)
  - enh: write Shape-Out version to exported .fcs and .tsv files (#250)

appveyor.yml

@@ -70,6 +70,7 @@ install:
   #- "conda update -f conda"
   # Anaconda client for searching packages?
   #- "conda install anaconda-client"
+  - conda config --append channels anaconda
   - "conda install --yes --quiet chaco enable kiwisolver numpy pip pyface pywin32 scipy wxpython"
   # workaround for build failures, see
   # https://ci.appveyor.com/project/paulmueller/shapeout/build/1.0.152#L504

docs/shapeout.bib

@@ -120,4 +120,13 @@ @Article{Otto2015
   publisher = {Springer Nature},
 }
 
+@Misc{FigshareRef,
+  author    = {Rosendahl, Philipp and Herold, Christoph and Müller, Paul and Guck, Jochen},
+  title     = {Real-time deformability cytometry reference data},
+  month     = {Feb},
+  year      = {2019},
+  doi       = {10.6084/m9.figshare.7771184.v2},
+  publisher = {figshare},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}

setup.py

@@ -46,7 +46,7 @@
                                ],
                       },
     install_requires=["appdirs",
-                      "dclab[all]>=0.14.6",
+                      "dclab[all]>=0.18.0",
                       "fcswrite>=0.5.0",
                       "h5py>=2.8.0",
                       "imageio>=2.3.0,<2.5.0",

shapeout/_version.py

@@ -1,20 +1,56 @@
 #!/usr/bin/env python
-"""Determine package version for git repositories from tags
-
-Each time this file is imported it checks if the ".git" folder is
-present and if so, obtains the version from the git history using
-`git describe`. This information is then stored in the file
-`_version_save.py` which is not versioned by git, but distributed
-along e.g. on PyPI.
+"""Determine package version from git repository tag
+
+Each time this file is imported it checks whether the package version
+can be determined using `git describe`. If this fails (because either
+this file is not located at the 1st level down the repository root or
+it is not under version control), the version is read from the script
+"_version_save.py" which is not versioned by git, but always included
+in the final distribution archive (e.g. via PyPI). If the git version
+does not match the saved version, then "_version_save.py" is updated.
+
+
+Usage
+-----
+1. Put this file in your main module directory:
+
+    REPO_ROOT/package_name/_version.py
+
+2. Add this line to REPO_ROOT/package_name/__init__.py
+
+    from ._version import version as __version__  # noqa: F401
+
+3. (Optional) Add this line to REPO_ROOT/.gitignore
+
+    _version_save.py
+
+Features
+--------
+- supports Python 2 and 3
+- supports frozen applications (e.g. PyInstaller)
+- supports installing into a virtual environment that is located in
+  a git repository
+- saved version is located in a python file and therefore no other
+  files (e.g. MANIFEST.in) need be edited
+- fallback version is the creation date
+- excluded from code coverage via "pragma: no cover"
+
+Changelog
+---------
+2019-11-06.2
+ - use os.path.split instead of counting os.path.sep (Windows)
+2019-11-06
+ - remove deprecated imp dependency (replace with parser)
+ - check whether this file is versioned and its location is correct
+ - code cleanup and docs update
 """
 from __future__ import print_function
 
 # Put the entire script into a `True` statement and add the hint
 # `pragma: no cover` to ignore code coverage here.
 if True:  # pragma: no cover
-    import imp
     import os
-    from os.path import abspath, basename, dirname, join
+    from os.path import abspath, basename, dirname, join, split
     import subprocess
     import sys
     import time
@@ -33,7 +69,7 @@ def git_describe():
         ourdir = dirname(abspath(__file__))
 
         def _minimal_ext_cmd(cmd):
-            # construct minimal environment
+            # Construct minimal environment
             env = {}
             for k in ['SYSTEMROOT', 'PATH']:
                 v = os.environ.get(k)
@@ -48,19 +84,33 @@ def _minimal_ext_cmd(cmd):
                                    stderr=subprocess.PIPE,
                                    env=env)
             out = pop.communicate()[0]
-            return out
+            return out.strip().decode('ascii', errors="ignore")
 
         # change directory
         olddir = abspath(os.curdir)
         os.chdir(ourdir)
 
+        # Make sure that we are getting "git describe" from our own
+        # repository (and not from a repository where we just happen
+        # to be in the directory tree).
+        git_revision = ""
         try:
-            out = _minimal_ext_cmd(['git', 'describe', '--tags', 'HEAD'])
-            git_revision = out.strip().decode('ascii')
+            # If this file is not under version control, "loc" will
+            # be empty.
+            loc = _minimal_ext_cmd(['git', 'ls-files', '--full-name',
+                                    __file__])
+            # If it is under version control, it should be located
+            # one hierarchy down from the repository root (either
+            # __file__ is "docs/conf.py" or "package_name/_version.py".
+            if len(split(loc)) == 2:
+                try:
+                    git_revision = _minimal_ext_cmd(['git', 'describe',
+                                                     '--tags', 'HEAD'])
+                except OSError:
+                    pass
         except OSError:
-            git_revision = ""
-
-        # go back to original directory
+            pass
+        # Go back to original directory
         os.chdir(olddir)
 
         return git_revision
@@ -69,8 +119,11 @@ def load_version(versionfile):
         """load version from version_save.py"""
         longversion = ""
         try:
-            _version_save = imp.load_source("_version_save", versionfile)
-            longversion = _version_save.longversion
+            with open(versionfile, "r") as fd:
+                data = fd.readlines()
+                for line in data:
+                    if line.startswith("longversion"):
+                        longversion = line.split("=")[1].strip().strip("'")
         except BaseException:
             try:
                 from ._version_save import longversion
@@ -82,7 +135,7 @@ def load_version(versionfile):
 
         return longversion
 
-    def save_version(version, versionfile):
+    def write_version(version, versionfile):
         """save version to version_save.py"""
         data = "#!/usr/bin/env python\n" \
             + "# This file was created automatically\n" \
@@ -91,8 +144,11 @@ def save_version(version, versionfile):
             with open(versionfile, "w") as fd:
                 fd.write(data.format(VERSION=version))
         except BaseException:
-            msg = "Could not write package version to {}.".format(versionfile)
-            warnings.warn(msg)
+            if not os.path.exists(versionfile):
+                # Only issue a warning if the file does not exist.
+                msg = "Could not write package version to {}.".format(
+                    versionfile)
+                warnings.warn(msg)
 
     hdir = dirname(abspath(__file__))
     if basename(__file__) == "conf.py" and "name" in locals():
@@ -116,7 +172,7 @@ def save_version(version, versionfile):
 
     # 2. previously created version file
     if longversion == "":
-        # Either this is this is not a git repository or we are in the
+        # Either this is not a git repository or we are in the
         # wrong git repository.
         # Get the version from the previously generated `_version_save.py`
         longversion = load_version(versionfile)
@@ -135,7 +191,7 @@ def save_version(version, versionfile):
         # This is only done if the program is not frozen (with e.g.
         # pyinstaller),
         if longversion != load_version(versionfile):
-            save_version(longversion, versionfile)
+            write_version(longversion, versionfile)
 
     # PEP 440-conform development version:
     version = ".post".join(longversion.split("-")[:2])

shapeout/gui/batch.py

@@ -245,9 +245,7 @@ def OnBrowse(self, e=None):
             self.WXfold_text1.SetLabel(thepath)
             self.parent.config.set_path(thepath, "BatchFD")
             # Search directory
-            tree, _cols = meta_tool.collect_data_tree(thepath)
-            self.data_files = [ t[1][1] for t in tree ]
-
+            self.data_files = meta_tool.find_data(thepath)
             if self.out_tsv_file is not None:
                 self.btnbatch.Enable()
             wx.EndBusyCursor()

shapeout/gui/controls.py

@@ -59,9 +59,9 @@ def AddSubpanels(self):
         self.subpanels.append(page_info)
         self.page_info = page_info
 
-        self.page_filter = SubPanelCalculate(notebook, funcparent=self)
-        notebook.AddPage(self.page_filter, "Calculate")
-        self.subpanels.append(self.page_filter)
+        self.page_calc = SubPanelCalculate(notebook, funcparent=self)
+        notebook.AddPage(self.page_calc, "Calculate")
+        self.subpanels.append(self.page_calc)
 
         self.page_filter = SubPanelFilter(notebook, funcparent=self)
         notebook.AddPage(self.page_filter, "Filter")
@@ -231,7 +231,7 @@ def OnPolygonFilter(self, result):
         uid = pf.unique_id
         mcur = result["measurement"]
         # update list of polygon filters
-        self.UpdatePages()
+        self.page_filter.UpdatePanel()
         # Determine the number of existing polygon filters
         npol = len(dclab.PolygonFilter.instances)
 
@@ -243,7 +243,6 @@ def OnPolygonFilter(self, result):
         else:
             # apply only to this one data set
             mcur.config["filtering"]["polygon filters"].append(uid)
-        self.OnChangeFilter()
 
 
     def Reset(self, key, subkeys=[]):
@@ -262,6 +261,7 @@ def Reset(self, key, subkeys=[]):
     def UpdatePages(self):
         """ fills pages """
         sel = self.notebook.GetSelection()
+        self.Freeze()
 
         # Update page content        
         for page in self.subpanels:
@@ -280,6 +280,5 @@ def UpdatePages(self):
         self.notebook.Layout()
         self.notebook.Refresh()
         self.notebook.Update()
-
         self.Layout()
-
+        self.Thaw()

shapeout/gui/controls_analyze.py

@@ -301,12 +301,11 @@ def update_classification(self):
             wxrep.SetValue(mm.config["analysis"]["regression repetition"])
 
 
-    def UpdatePanel(self, analysis=None):
+    def RepopulatePanel(self, analysis=None):
+        self.ClearSubPanel()
         if analysis is None:
             analysis = self.analysis
         self.analysis = analysis
-
-        self.ClearSubPanel()
 
         sizer = wx.BoxSizer(wx.HORIZONTAL)
 
@@ -332,5 +331,3 @@ def UpdatePanel(self, analysis=None):
 
         self.SetSizer(sizer)
         sizer.Fit(self)
-        self.Layout()
-        self.UpdateScrolling()

shapeout/gui/controls_calculate.py

@@ -178,12 +178,11 @@ def OnComputeEmodulus(self, e=None):
         self.funcparent.OnChangeFilter()
 
 
-    def UpdatePanel(self, analysis=None):
+    def RepopulatePanel(self, analysis=None):
+        self.ClearSubPanel()
         if analysis is None:
             analysis = self.analysis
         self.analysis = analysis
-
-        self.ClearSubPanel()
 
         sizer = wx.BoxSizer(wx.HORIZONTAL)
         emodbox = self.make_emodulus_choices(analysis)

shapeout/gui/controls_contourplot.py

@@ -99,9 +99,8 @@ def _box_from_cfg_contour(self, analysis):
         return mastersizer
 
 
-    def UpdatePanel(self, analysis):
+    def RepopulatePanel(self, analysis):
         self.ClearSubPanel()
-
         # sizer
         sizer = wx.BoxSizer(wx.HORIZONTAL)
         fbox = self._box_from_cfg_contour(analysis)

shapeout/gui/controls_filter.py

@@ -520,7 +520,7 @@ def OnPolygonWindow(self, e=None):
         ldw.Show()
 
 
-    def UpdatePanel(self, analysis=None):
+    def RepopulatePanel(self, analysis=None):
         if analysis is None:
             # previous analysis is used
             analysis = self.analysis
@@ -529,10 +529,9 @@ def UpdatePanel(self, analysis=None):
         else:
             old_meas_selection = 0
 
-        self.analysis = analysis
-
         self.ClearSubPanel()
 
+        self.analysis = analysis
 
         sizer = wx.BoxSizer(wx.HORIZONTAL)
 

shapeout/gui/controls_info.py

@@ -25,10 +25,8 @@ class SubPanelInfo(SubPanel):
     def __init__(self, *args, **kwargs):
         SubPanel.__init__(self, *args, **kwargs)
 
-    def UpdatePanel(self, analysis):
-        """  """
+    def RepopulatePanel(self, analysis=None):
         self.ClearSubPanel()
-
         # Create three boxes containing information
         sizer = wx.BoxSizer(wx.HORIZONTAL)
         genbox = self._box_from_cfg_read(analysis, "experiment", ignore=HIDDEN)
@@ -56,4 +54,3 @@ def UpdatePanel(self, analysis):
         sizer.Add(flbox)
         self.SetSizer(sizer)
         sizer.Fit(self)
-

shapeout/gui/controls_plotting.py

@@ -306,11 +306,8 @@ def OnApply(self, e=None):
         self.funcparent.OnChangePlot(e)
 
 
-    def UpdatePanel(self, analysis):
-        """  """
+    def RepopulatePanel(self, analysis=None):
         self.ClearSubPanel()
-
-        # sizer
         sizer = wx.BoxSizer(wx.HORIZONTAL)
         plotsizer = self._box_from_cfg_plotting(analysis)
         ordersizer = self._box_order_plots(analysis, sizey=plotsizer.GetMinSize()[1]-25)

shapeout/gui/controls_scatterplot.py

@@ -50,10 +50,9 @@ def _box_from_cfg_scatter(self, analysis):
         return mastersizer
 
 
-    def UpdatePanel(self, analysis):
+    def RepopulatePanel(self, analysis):
         """Redraw the entire panel"""
         self.ClearSubPanel()
-
         # sizer
         sizer = wx.BoxSizer(wx.HORIZONTAL)
         fbox = self._box_from_cfg_scatter(analysis)

shapeout/gui/controls_statistics.py

@@ -60,9 +60,7 @@ def _box_statistics(self, analysis):
             sizer.Layout()
         return sizer
 
-
-    def UpdatePanel(self, analysis):
-        """  """
+    def RepopulatePanel(self, analysis):
         self.ClearSubPanel()
         # Create three boxes containing information
         sizer = wx.BoxSizer(wx.HORIZONTAL)