Fix Tkinter issues and update all environments and github workflows to Python 3.11

.github/workflows/manual-pages-deploy.yml

@@ -28,7 +28,7 @@ jobs:
     - name: Setup Miniconda
       uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: '3.10'
+        python-version: '3.11'
         environment-file: docs/environment.yml
         auto-activate: true
         activate-environment: sphinx

.github/workflows/pages-deploy-from-docs.yml

@@ -30,7 +30,7 @@ jobs:
     - name: Setup Miniconda
       uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: '3.10'
+        python-version: '3.11'
         environment-file: docs/environment.yml
         auto-activate: true
         activate-environment: sphinx

.github/workflows/pages-deploy.yml

@@ -30,7 +30,7 @@ jobs:
     - name: Setup Miniconda
       uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: '3.10'
+        python-version: '3.11'
         environment-file: docs/environment.yml
         auto-activate: true
         activate-environment: sphinx

.github/workflows/pypi-pyblish.yaml

@@ -20,10 +20,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.8
+    - name: Set up Python 3.11
       uses: actions/setup-python@v3
       with:
-        python-version: '3.8'
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

CHAP/common/processor.py

@@ -390,6 +390,19 @@ def confirm(event):
             """Callback function for the "Confirm" button."""
             plt.close()
 
+        def on_close(event):
+            """Callback function to disconnect and remove all widgets."""
+            # Disconnect all widget callbacks when figure is closed
+            lambda_box.disconnect(lambda_cid)
+            continue_btn.disconnect(continue_cid)
+            confirm_btn.disconnect(confirm_cid)
+
+            # ... and remove the buttons before returning the figure
+            lambda_box.ax.remove()
+            continue_btn.ax.remove()
+            confirm_btn.ax.remove()
+
+
         def get_baseline(
                 y, *, mask=None, w=None, tol=1.e-6, lam=1.6, max_iter=20):
             """Get a baseline.
@@ -484,19 +497,12 @@ def get_baseline(
                 plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm')
             confirm_cid = confirm_btn.on_clicked(confirm)
 
+            # Connect the close event callback to the canvas
+            fig.canvas.mpl_connect('close_event', on_close)
+
             # Show figure for user interaction
             plt.show()
 
-            # Disconnect all widget callbacks when figure is closed
-            lambda_box.disconnect(lambda_cid)
-            continue_btn.disconnect(continue_cid)
-            confirm_btn.disconnect(confirm_cid)
-
-            # ... and remove the buttons before returning the figure
-            lambda_box.ax.remove()
-            continue_btn.ax.remove()
-            confirm_btn.ax.remove()
-
         if return_buf:
             fig_title.set_in_layout(True)
             fig_subtitles[-1].set_in_layout(True)

CHAP/edd/environment.yml

@@ -4,20 +4,17 @@ channels:
   - hexrd
   - nodefaults
 dependencies:
-  - python>=3.9,<3.11
-  - asteval==1.0.8
-  - chessanalysispipeline
-  - hexrd==0.9.4
+  - python==3.11
+  - numpy==2.4.6
+  - pydantic==2.13.5
+  - pyyaml==6.0.3
+  - hexrd==0.10.6
   - lmfit==1.3.4
-  - matplotlib==3.10.8
-  - mpi4py==4.1.1
-  - nexpy==2.0.0
-  - nexusformat==2.0.0
-  - pip==25.3
-  - pydantic==2.12.5
-  - requests==2.32.5
-  - scipy==1.15.2
+  - nexpy==2.1.0
+  - nexusformat==2.1.0
+  - pip==26.2.1
+  - scipy==1.17.1
   - sympy==1.14.0
   - pip:
-    - certif-pyspec==1.5.3
     - chess-scanparsers
+    - chessanalysispipeline

CHAP/edd/processor.py

@@ -1580,6 +1580,17 @@ def confirm(event):
                 error_texts.pop()
             plt.close()
 
+        def on_close(event):
+            """Callback function to disconnect and remove all widgets."""
+            # Disconnect all widget callbacks when figure is closed
+            reset_btn.disconnect(reset_cid)
+            confirm_btn.disconnect(confirm_cid)
+
+            # ... and remove the buttons before returning the figure
+            reset_btn.ax.remove()
+            confirm_btn.ax.remove()
+
+
         def find_peaks(min_height=0.05, min_width=5, tolerance=10):
             """Find the peaks.
 
@@ -1739,15 +1750,10 @@ def select_peaks():
                 plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm')
             confirm_cid = confirm_btn.on_clicked(confirm)
 
-            plt.show()
-
-            # Disconnect all widget callbacks when figure is closed
-            reset_btn.disconnect(reset_cid)
-            confirm_btn.disconnect(confirm_cid)
+            # Connect the close event callback to the canvas
+            fig.canvas.mpl_connect('close_event', on_close)
 
-            # ... and remove the buttons before returning the figure
-            reset_btn.ax.remove()
-            confirm_btn.ax.remove()
+            plt.show()
 
         if return_buf:
             fig_title[0].set_in_layout(True)

CHAP/edd/utils.py

@@ -217,6 +217,16 @@ def confirm(event):
         """Callback function for the "Confirm" button."""
         plt.close()
 
+    def on_close(event):
+        """Callback function to disconnect and remove all widgets."""
+        # Disconnect all widget callbacks when figure is closed
+        tth_input.disconnect(cid_update_tth)
+        confirm_btn.disconnect(confirm_cid)
+
+        # ...and remove the buttons before returning the figure
+        tth_input.ax.remove()
+        confirm_btn.ax.remove()
+
     fig_title = []
     error_texts = []
 
@@ -268,17 +278,12 @@ def confirm(event):
         confirm_btn = Button(plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm')
         confirm_cid = confirm_btn.on_clicked(confirm)
 
+        # Connect the close event callback to the canvas
+        fig.canvas.mpl_connect('close_event', on_close)
+
         # Show figure for user interaction
         plt.show()
 
-        # Disconnect all widget callbacks when figure is closed
-        tth_input.disconnect(cid_update_tth)
-        confirm_btn.disconnect(confirm_cid)
-
-        # ...and remove the buttons before returning the figure
-        tth_input.ax.remove()
-        confirm_btn.ax.remove()
-
     # Save the figures if requested and close
     if return_buf:
         if interactive:
@@ -1100,6 +1105,19 @@ def confirm(event):
                                      f'detector {detector_id}')
                 plt.close()
 
+        def on_close(event):
+            """Callback function to disconnect and remove all widgets."""
+            # Disconnect all widget callbacks when figure is closed
+            add_span_btn.disconnect(add_span_cid)
+            fig.canvas.mpl_disconnect(pick_hkl_cid)
+            reset_btn.disconnect(reset_cid)
+            confirm_btn.disconnect(confirm_cid)
+
+            # ...and remove the buttons before returning the figure
+            add_span_btn.ax.remove()
+            confirm_btn.ax.remove()
+            reset_btn.ax.remove()
+
         if detector_id is None:
             _change_fig_title('Select data and HKLs to use in fitting')
         else:
@@ -1125,19 +1143,11 @@ def confirm(event):
         confirm_btn = Button(plt.axes([0.75, 0.05, 0.15, 0.075]), 'Confirm')
         confirm_cid = confirm_btn.on_clicked(confirm)
 
+        # Connect the close event callback to the canvas
+        fig.canvas.mpl_connect('close_event', on_close)
+
         # Show figure for user interaction
         plt.show()
-
-        # Disconnect all widget callbacks when figure is closed
-        add_span_btn.disconnect(add_span_cid)
-        fig.canvas.mpl_disconnect(pick_hkl_cid)
-        reset_btn.disconnect(reset_cid)
-        confirm_btn.disconnect(confirm_cid)
-
-        # ...and remove the buttons before returning the figure
-        add_span_btn.ax.remove()
-        confirm_btn.ax.remove()
-        reset_btn.ax.remove()
         plt.subplots_adjust(bottom=0.0)
 
     if return_buf:

CHAP/giwaxs/environment.yml

@@ -3,13 +3,14 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python>=3.9,<3.11
-  - chessanalysispipeline
-  - nexpy==2.0.0
-  - nexusformat==2.0.0
-  - pip==25.3
-  - pyfai==2026.2.0
-  - pydantic==2.12.5
+  - python==3.11
+  - numpy==2.4.6
+  - pydantic==2.13.5
+  - pyyaml==6.0.3
+  - nexpy==2.1.0
+  - nexusformat==2.1.0
+  - pip==26.2.1
+  - pyfai==2026.9.0
   - pip:
-    - certif-pyspec==1.5.3
     - chess-scanparsers
+    - chessanalysispipeline

CHAP/saxswaxs/environment.yml

@@ -4,14 +4,17 @@ channels:
   - nodefaults
 dependencies:
   - python==3.11
-#  - chessanalysispipeline
-  - nexpy==1.0.9
-  - nexusformat==1.0.6
-  - pandas==2.3.3
-  - pip==24.2
-  - pydantic==2.7.3
-  - pyfai==2025.1.0
-  - zarr==3.0.6
+  - numpy==2.4.6
+  - pydantic==2.13.5
+  - pyyaml==6.0.3
+  - lmfit==1.3.4
+  - nexpy==2.1.0
+  - nexusformat==2.1.0
+  - pip==26.2.1
+  - pyfai==2026.9.0
+  - scipy==1.17.1
+  - sympy==1.14.0
+  - zarr==3.1.6
   - pip:
-    - certif-pyspec==1.5.3
-#    - chess-scanparsers
+    - chess-scanparsers
+    - chessanalysispipeline

CHAP/tomo/environment.yml

@@ -4,22 +4,18 @@ channels:
   - astra-toolbox
   - nodefaults
 dependencies:
-  - python>=3.9,<3.11
-  - astra-toolbox==2.3.1
-  - chessanalysispipeline
-  - fabio==2025.10.0
+  - python==3.11
+  - numpy==2.4.6
+  - pydantic==2.13.5
+  - pyyaml==6.0.3
+  - astra-toolbox==2.5.0
   - lmfit==1.3.4
-  - matplotlib==3.10.8
-  - mpi4py==4.1.1
-  - nexpy==2.0.0
-  - nexusformat==2.0.0
-  - pip==25.3
-  - pyfai==2025.12.1
-  - pydantic==2.12.5
-  - requests==2.32.5
-  - scipy==1.15.2
+  - nexpy==2.1.0
+  - nexusformat==2.1.0
+  - pip==26.2.1
+  - scipy==1.17.1
   - sympy==1.14.0
   - tomopy==1.15.3
   - pip:
-    - certif-pyspec==1.5.3
     - chess-scanparsers
+    - chessanalysispipeline