Merge pull request #17 from JacksonBurns/bugs-dev

Fixing bugs with the legend, empty wells, and memory leaks in `Present`.

.github/workflows/run_extended_present_tests.yml

@@ -0,0 +1,31 @@
+name: Run Extended Present Tests
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Install Dependencies
+        run: |
+          sudo apt-get install python3-tk
+          conda install python=3.8
+          python -m pip install -r requirements.txt
+          python -m pip install -e .
+          python -m pip install coverage
+      
+      - name: Run Tests
+        uses: GabrielBB/xvfb-action@v1
+        with:
+          run: |
+            coverage run --source=. --omit=test/*,setup.py,crow/__main__.py -m unittest test/test_Present_2.py
+      - name: Show Coverage
+        run: |
+          coverage report -m

.github/workflows/run_present_tests.yml

@@ -0,0 +1,31 @@
+name: Run Present Tests
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Install Dependencies
+        run: |
+          sudo apt-get install python3-tk
+          conda install python=3.8
+          python -m pip install -r requirements.txt
+          python -m pip install -e .
+          python -m pip install coverage
+      
+      - name: Run Tests
+        uses: GabrielBB/xvfb-action@v1
+        with:
+          run: |
+            coverage run --source=. --omit=test/*,setup.py,crow/__main__.py -m unittest test/test_Present.py
+      - name: Show Coverage
+        run: |
+          coverage report -m

.github/workflows/run_tests.yml

@@ -25,7 +25,7 @@ jobs:
         uses: GabrielBB/xvfb-action@v1
         with:
           run: |
-            coverage run --source=. --omit=test/*,setup.py,crow/__main__.py -m unittest discover
+            coverage run --source=. --omit=test/*,setup.py,crow/__main__.py -m unittest test/test_Crow.py
       - name: Show Coverage
         run: |
           coverage report -m

crow/__init__.py

@@ -1,4 +1,4 @@
 from . import uitabs
 from . import utils
 
-__version__ = "2.0.0"
+__version__ = "2.0.1"

crow/uitabs/Present.py

@@ -15,6 +15,10 @@
 from crow.utils.popupwindows.numberofcutoffs import numberofcutoffsPopup
 from crow.utils.popupwindows.shadebyyield import shadebyyieldPopup
 
+import matplotlib as mpl
+
+mpl.rcParams.update({'figure.max_open_warning': 0})
+
 
 class Present(tk.Frame):
     """
@@ -204,6 +208,8 @@ def presentdatacallback():
                     )
             else:
                 messagebox.showerror("Error!", "Please select a layout.")
+            # regardless of what happened, close active plots
+            plot.close('all')
 
         def draw_empty(subplt, row, col, wellnum, e):  # pragma: no cover
             """Draws an epty pie when an error is encountered.
@@ -215,7 +221,7 @@ def draw_empty(subplt, row, col, wellnum, e):  # pragma: no cover
                 wellnum (int): Index of well.
                 e (exception): exception that was raised to get here.
             """
-            subplt[row, col].pie([0])
+            subplt[row, col].pie([0], normalize=False)
             warningmessage = (
                 "Issue displaying well "
                 + str(wellnum + 1)
@@ -343,7 +349,9 @@ def graphic_generator(exceldata, subplotdims, totalcolormap, dims):
                 )
             else:
                 myfig, subplt = plot.subplots(
-                    subplotdims[0], subplotdims[1], figsize=dims
+                    subplotdims[0],
+                    subplotdims[1],
+                    figsize=(dims[1] * 2 * 12, dims[0] * 10),
                 )
             for wellnum in range(0, subplotdims[0] * subplotdims[1]):
                 # go to position
@@ -392,16 +400,30 @@ def graphic_generator(exceldata, subplotdims, totalcolormap, dims):
                     except Exception as e:
                         draw_empty(subplt, row, col, wellnum, e)
                 else:
-                    draw_filled(
-                        totalcolormap,
-                        welldata,
-                        subplt,
-                        row,
-                        col,
-                    )
+                    if not (any(i < 0 for i in welldata) or all(i == 0 for i in welldata)):
+                        draw_filled(
+                            totalcolormap,
+                            welldata,
+                            subplt,
+                            row,
+                            col,
+                        )
+                    else:
+                        draw_empty(
+                            subplt,
+                            row,
+                            col,
+                            wellnum,
+                            RuntimeWarning(
+                                "Well {wellnum} is blank or contains a negative number.",
+                            ),
+                        )
                 # write numbers accross the top
                 if row == 0:
-                    subplt[row, col].set_title(str(wellnum + 1))
+                    subplt[row, col].set_title(
+                        str(wellnum + 1),
+                        fontsize=90,
+                    )
                 # write letters across the left side
                 if col == 0:
                     subplt[row, col].set_ylabel(
@@ -410,6 +432,7 @@ def graphic_generator(exceldata, subplotdims, totalcolormap, dims):
                         ],
                         rotation=0,
                         labelpad=10,
+                        fontsize=90,
                     )
                 # draw the image over the well
                 if self.image_overlay.get():
@@ -428,12 +451,12 @@ def graphic_generator(exceldata, subplotdims, totalcolormap, dims):
                     end = len(headers)
                 for header in headers[:end]:
                     myfig.text(
-                        0.2 + 0.1 * count,
-                        0.98,
+                        1.05,
+                        0.8 - 0.05 * count,
                         header.replace("\n", ""),
-                        ha="center",
+                        ha="left",
                         va="bottom",
-                        size=12,
+                        size=90,
                         color=totalcolormap[count],
                         path_effects=[pe.withStroke(
                             linewidth=1, foreground='black')],

test/test_Crow.py

@@ -16,7 +16,6 @@
 from crow.utils.popupwindows.shadebyyield import shadebyyieldPopup
 from crow.uitabs.PrePull import PrePull
 from crow.uitabs.Pull import Pull
-from crow.uitabs.Present import Present
 
 
 class TestCrow(unittest.TestCase):
@@ -533,154 +532,6 @@ def test_Pull(self):
         os.remove("blank.xml")
         os.remove(".csv")
 
-    def test_Present(self):
-        """
-        Methods of the Present class.
-        """
-        # test all layouts
-        cg = crow_globals()
-        cg.datafiles = ["test/data/processed_96-well_data.csv"]
-        pres = Present("test present", cg)
-        pres.colorscheme.set(1)
-        pres.write_to_file.set(False)
-        for layout in range(1, 7):
-            pres.layout.set(layout)
-            with patch("crow.uitabs.Present.plot.show") as test_plot:
-                pres.presentbutton.invoke()
-                self.assertTrue(test_plot.called)
-        pres.layout.set(3)
-
-        # test all colormaps
-        for colormap in range(1, 4):
-            pres.colorscheme.set(colormap)
-            with patch("crow.uitabs.Present.plot.show") as test_plot:
-                pres.presentbutton.invoke()
-                self.assertTrue(test_plot.called)
-
-        # test image overlay
-        cg = crow_globals()
-        with open("test/data/processed_24-well_data_images.csv", "r") as file:
-            procdata = file.readlines()
-            with open("temp.csv", "w") as file2:
-                file2.write(procdata[0])
-                for line in procdata[1:]:
-                    file2.write(
-                        line.replace(
-                            '\n',
-                            "," + os.path.join(os.getcwd(), 'test', 'data', 'blank.png') + '\n'),
-                    )
-        cg.datafiles = ["temp.csv"]
-        pres = Present("test present", cg)
-        pres.colorscheme.set(1)
-        pres.write_to_file.set(False)
-        pres.layout.set(3)
-        pres.image_overlay.set(True)
-        with patch("crow.uitabs.Present.plot.show") as test_plot:
-            with open(os.devnull, 'w') as devnull:
-                with contextlib.redirect_stderr(devnull):
-                    # ignore resource warning
-                    pres.presentbutton.invoke()
-            self.assertTrue(test_plot.called)
-        os.remove("temp.csv")
-
-        # no colorscheme selected
-        cg = crow_globals()
-        cg.datafiles = ["test/data/processed_96-well_data.csv"]
-        pres = Present("test present", cg)
-        pres.write_to_file.set(False)
-        pres.layout.set(1)
-        with patch("crow.uitabs.Present.messagebox.showerror") as test_error:
-            pres.presentbutton.invoke()
-            self.assertTrue(test_error.called)
-
-        # save to file
-        cg = crow_globals()
-        cg.datafiles = ["test/data/processed_96-well_data.csv"]
-        pres = Present("test present", cg)
-        pres.write_to_file.set(True)
-        pres.colorscheme.set(1)
-        pres.layout.set(3)
-        with patch("crow.uitabs.Present.messagebox.showinfo") as test_info:
-            with patch("crow.uitabs.Present.savefig") as test_save:
-                with patch("crow.uitabs.Present.webbrowser.open") as test_open:
-                    pres.presentbutton.invoke()
-                    self.assertTrue(test_info.called)
-                    self.assertTrue(test_save.called)
-                    self.assertTrue(test_open.called)
-
-        # no layout selected
-        cg = crow_globals()
-        cg.datafiles = ["test/data/processed_96-well_data.csv"]
-        pres = Present("test present", cg)
-        pres.write_to_file.set(False)
-        pres.colorscheme.set(1)
-        with patch("crow.uitabs.Present.messagebox.showerror") as test_error:
-            pres.presentbutton.invoke()
-            self.assertTrue(test_error.called)
-
-        # test all layouts with error
-        cg = crow_globals()
-        cg.datafiles = ["test/data/processed_96-well_data_with_errors.csv"]
-        pres = Present("test present", cg)
-        pres.colorscheme.set(1)
-        pres.write_to_file.set(False)
-        for layout in range(1, 7):
-            pres.layout.set(layout)
-            with patch("crow.uitabs.Present.messagebox.showerror") as test_error:
-                with patch("crow.uitabs.Present.mylog") as test_logger:
-                    pres.presentbutton.invoke()
-                    self.assertTrue(test_error.called)
-                    self.assertTrue(test_logger.called)
-
-        # wrong data type
-        cg = crow_globals()
-        cg.datafiles = ["test/data/raw_data_1.xml"]
-        pres = Present("test present", cg)
-        pres.write_to_file.set(False)
-        pres.layout.set(1)
-        pres.colorscheme.set(1)
-        with patch("crow.uitabs.Present.messagebox.showerror") as test_error:
-            pres.presentbutton.invoke()
-            self.assertTrue(test_error.called)
-
-        # no data selected
-        cg = crow_globals()
-        cg.datafiles = []
-        pres = Present("test present", cg)
-        pres.write_to_file.set(False)
-        pres.layout.set(1)
-        pres.colorscheme.set(1)
-        with patch("crow.uitabs.Present.messagebox.showerror") as test_error:
-            pres.presentbutton.invoke()
-            self.assertTrue(test_error.called)
-
-        # too many input files
-        cg = crow_globals()
-        cg.datafiles = [
-            "test/data/processed_96-well_data_with_errors.csv",
-            "test/data/processed_96-well_data.csv",
-        ]
-        pres = Present("test present", cg)
-        pres.write_to_file.set(False)
-        pres.layout.set(1)
-        pres.colorscheme.set(1)
-        with patch("crow.uitabs.Present.messagebox.showerror") as test_error:
-            pres.presentbutton.invoke()
-            self.assertTrue(test_error.called)
-
-        # input file too big
-        cg = crow_globals()
-        cg.datafiles = [
-            "test/data/processed_too_big.csv"
-        ]
-        pres = Present("test present", cg)
-        pres.write_to_file.set(False)
-        pres.layout.set(1)
-        pres.colorscheme.set(1)
-        with patch("crow.uitabs.Present.messagebox.showerror") as test_error:
-            pres.presentbutton.invoke()
-            self.assertTrue(test_error.called)
-
     def test_cutoff(self):
         """
         Launch the popup for getting the cutoff value in present