Flake fixes pt4

.github/workflows/docs.yml

@@ -0,0 +1,43 @@
+name: Build Documentation
+
+on:
+  push:
+    branches:
+      - main
+  release:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: build
+          auto-update-conda: true
+
+      - name: install requirements
+        run: >-
+          conda install -n build -c conda-forge
+          --file requirements/build.txt
+          --file requirements/run.txt
+          --file requirements/docs.txt
+          --quiet --yes
+
+      - name: install the package
+        run: python -m pip install . --no-deps
+
+      - name: build documents
+        run: make -C doc html
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc/build/html

.github/workflows/main.yml

@@ -0,0 +1,53 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - CI
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  miniconda:
+    name: Miniconda ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: ["ubuntu-latest"]
+    steps:
+      - name: check out diffpy.pdfgui
+        uses: actions/checkout@v3
+        with:
+          repository: diffpy/diffpy.pdfgui
+          path: .
+          fetch-depth: 0  # avoid shallow clone with no tags
+
+      - name: Install Mamba
+        run: |
+          wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh" -O mambaforge.sh
+          bash mambaforge.sh -b -p $HOME/mambaforge
+          echo "$HOME/mambaforge/bin" >> $GITHUB_PATH
+          source $HOME/mambaforge/etc/profile.d/conda.sh
+          conda init bash
+
+      - name: Create conda environment
+        run: |
+          source $HOME/mambaforge/etc/profile.d/conda.sh
+          conda create -n test_env python=3.12 xonsh regolith -c conda-forge -y
+          conda activate test_env
+          pip install case_insensitive_dict
+
+      - name: Install dependencies
+        run: |
+          source $HOME/mambaforge/etc/profile.d/conda.sh
+          conda activate test_env
+          mamba install --file requirements/run.txt
+          mamba install --file requirements/test.txt
+          pip install -e .
+
+      - name: Use Xvfb Action
+        uses: GabrielBB/xvfb-action@v1
+        with:
+          run: |
+            bash -c "source $HOME/mambaforge/etc/profile.d/conda.sh && conda activate test_env && python -m run_tests.py"

.github/workflows/pre-commit.yml

@@ -0,0 +1,19 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+  workflow_dispatch:
+
+jobs:
+  pre-commit:
+    # pull requests are a duplicate of a branch push if within the same repo.
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --all-files

conda-recipe/meta.yaml → conda-recipe/meta.suppress_yaml

@@ -54,7 +54,7 @@ test:
     # entry points work.
 
 
-  # You can also put a file called run_test.py in the recipe that will be run
+  # You can also put a file called dont_run.py in the recipe that will be run
   # at test time.
 
   # requires:

environment.yml

@@ -0,0 +1,6 @@
+name: diffpy.pdfgui
+channels:
+  - conda-forge
+dependencies:
+  - python=3
+  - pip

requirements/run.txt

@@ -1,4 +1,4 @@
-numpy
+numpy==1.26
 wxpython
 diffpy.pdffit2
 diffpy.utils

requirements/test.txt

@@ -1,2 +1,4 @@
 pytest
 freezegun
+coverage
+codecov

run_tests.py

@@ -0,0 +1,5 @@
+#!/usr/bin/env python
+
+import diffpy.pdfgui.tests
+
+assert diffpy.pdfgui.tests.testdeps().wasSuccessful()

src/diffpy/pdfgui/applications/__init__.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2009 Trustees of the Columbia University
+#                   (c) 2009-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

src/diffpy/pdfgui/control/structureviewer.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2009 Trustees of the Columbia University
+#                   (c) 2009-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

src/diffpy/pdfgui/gui/aboutdialog.py

@@ -4,6 +4,8 @@
 # PDFgui            by DANSE Diffraction group
 #                   Simon J. L. Billinge
 #                   (c) 2006 trustees of the Michigan State University.
+#                   (c) 2024 trustees of the Columbia University in the City
+#                   of New York
 #                   All rights reserved.
 #
 # File coded by:    Dmitriy Bryndin
@@ -233,7 +235,7 @@ def onColumbiaLogo(self, event):  # wxGlade: DialogAbout.<event_handler>
 
 # end of class DialogAbout
 
-##### testing code ###########################################################
+# #### testing code ###########################################################
 
 if __name__ == "__main__":
     app = wx.App()

src/diffpy/pdfgui/gui/adddatapanel.py

@@ -5,6 +5,7 @@
 # PDFgui            by DANSE Diffraction group
 #                   Simon J. L. Billinge
 #                   (c) 2006 trustees of the Michigan State University.
+#                   (c) 2024 trustees of the Columbia University in the City
 #                   All rights reserved.
 #
 # File coded by:    Chris Farrow

src/diffpy/pdfgui/gui/errorwrapper.py

@@ -75,7 +75,7 @@ def _f(*args, **kwargs):
             return rvpass
 
         # Everything else
-        except:
+        except Exception:
             if pdfguiglobals.dbopts.pythondebugger:
                 import pdb
 

src/diffpy/pdfgui/gui/fittree.py

@@ -356,9 +356,9 @@ def AddFit(self, fitname="Fit 1", cdata=None, paste=False):
                 cdata = self.control.paste(cdata, None, fitname, pos)
             self.SetControlData(newfit, cdata)
             return newfit
-        except:
+        except Exception:
             self.Delete(newfit)
-            raise
+            raise Exception
         return
 
     def AddPhase(self, node, label, insertafter=None, filename=None, makedata=True, cdata=None):
@@ -427,9 +427,9 @@ def AddPhase(self, node, label, insertafter=None, filename=None, makedata=True,
             elif cdata is not None:
                 self.control.paste(cdata, pdata, label, pos)
             return newphase
-        except:
+        except Exception:
             self.Delete(newphase)
-            raise
+            raise Exception
         return
 
     def AddDataSet(self, node, label, insertafter=None, filename=None, makedata=True, cdata=None):
@@ -492,9 +492,9 @@ def AddDataSet(self, node, label, insertafter=None, filename=None, makedata=True
             elif cdata is not None:
                 self.control.paste(cdata, pdata, label, pos)
             return newset
-        except:
+        except Exception:
             self.Delete(newset)
-            raise
+            raise Exception
         return
 
     def AddCalc(self, node, label, insertafter=None, makedata=True, cdata=None):
@@ -553,9 +553,9 @@ def AddCalc(self, node, label, insertafter=None, makedata=True, cdata=None):
             elif cdata is not None:
                 self.control.paste(cdata, pdata, label, pos)
             return newcalc
-        except:
+        except Exception:
             self.Delete(newcalc)
-            raise
+            raise Exception
         return
 
     def CopyBranch(self, startnode):
@@ -611,7 +611,7 @@ def GetClipboard(self):
             if cdatabytes[:16] == "pdfgui_cliboard=".encode():
                 cdatabytes = cdatabytes[16:]
                 cdata = pickle_loads(cdatabytes)
-        except:
+        except Exception:
             pass
         return cdata
 

src/diffpy/pdfgui/gui/phasepanelutils.py

@@ -234,7 +234,7 @@ def canPasteIntoCells(panel):
         # Strip any trailing tabs
         rowlist = [r.rstrip("\t") for r in rowlist]
         celllist = [r.split("\t") for r in rowlist]
-    except:
+    except wx.PyDeadObjectError:
         return False
 
     if len(celllist) == 0:

src/diffpy/pdfgui/gui/plotpanel.py

@@ -16,8 +16,6 @@
 
 # generated by wxGlade 0.9.3 on Fri Jul 19 16:05:24 2019
 
-import sys
-
 import wx
 
 from diffpy.pdfgui.control.controlerrors import ControlConfigError
@@ -167,7 +165,7 @@ def _represent(mixedNames):
         xvals = _represent(xdata)
         try:
             xvals.remove("rw")
-        except:
+        except ValueError:
             pass
         numericStringSort(xvals)
 

src/diffpy/pdfgui/gui/wxextensions/wx12.py

@@ -46,7 +46,9 @@ def Append(self, *args, **kwargs):
 
 
 if WX4:
-    Menu = wx.Menu
+    RealMenu = wx.Menu
+else:
+    RealMenu = Menu
 
 # ----------------------------------------------------------------------------
 
@@ -58,7 +60,9 @@ class ListCtrl(wx.ListCtrl):
 
 
 if WX4:
-    ListCtrl = wx.ListCtrl
+    RealListCtrl = wx.ListCtrl
+else:
+    RealListCtrl = ListCtrl
 
 # ----------------------------------------------------------------------------
 
@@ -70,7 +74,9 @@ class TreeCtrl(wx.TreeCtrl):
 
 
 if WX4:
-    TreeCtrl = wx.TreeCtrl
+    RealTreeCtrl = wx.TreeCtrl
+else:
+    RealTreeCtrl = TreeCtrl
 
 # wx.ToolBar -----------------------------------------------------------------
 
@@ -92,6 +98,6 @@ def patchToolBarMethods(toolbar):
 
 # Final checks ---------------------------------------------------------------
 
-assert WX3 ^ (Menu is wx.Menu)
-assert WX3 ^ (TreeCtrl is wx.TreeCtrl)
-assert WX3 ^ (ListCtrl is wx.ListCtrl)
+assert WX3 ^ (RealMenu is wx.Menu)
+assert WX3 ^ (RealTreeCtrl is wx.TreeCtrl)
+assert WX3 ^ (RealListCtrl is wx.ListCtrl)

src/diffpy/pdfgui/tests/__init__.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2012 Trustees of the Columbia University
+#                   (c) 2012-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

src/diffpy/pdfgui/tests/run.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2012 Trustees of the Columbia University
+#                   (c) 2012-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

src/diffpy/pdfgui/tests/rundeps.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2012 Trustees of the Columbia University
+#                   (c) 2012-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

src/diffpy/pdfgui/tests/showphasenotebookpanel.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2016 Trustees of the Columbia University
+#                   (c) 2016-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas

src/diffpy/pdfgui/tests/testutils.py

@@ -3,7 +3,7 @@
 #
 # diffpy.pdfgui     by DANSE Diffraction group
 #                   Simon J. L. Billinge
-#                   (c) 2016 Trustees of the Columbia University
+#                   (c) 2016-2024 Trustees of the Columbia University
 #                   in the City of New York.  All rights reserved.
 #
 # File coded by:    Pavol Juhas