chore: merge main py311 update

biorack · Feb 15, 2024 · 677821f · 677821f
2 parents ccbef9d + 960d7cf
commit 677821f
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Showing 9 changed files with 18 additions and 13 deletions.
diff --git a/docker/Dockerfile.ci b/docker/Dockerfile.ci
@@ -70,7 +70,7 @@ RUN curl $FLAGS -O "$BASE_DATA_URL/20210915_JGI-AK_MK_506588_SoilWaterRep_final_
     && curl $FLAGS -O "$BASE_DATA_URL/20210915_JGI-AK_MK_506588_SoilWaterRep_final_QE-HF_C18_USDAY63680_NEG_MSMS_63_Neg-D89_C_Rg80to1200-CE102040-soil-S1_Run215.h5" \
     && curl $FLAGS -O "$BASE_DATA_URL/20210915_JGI-AK_MK_506588_SoilWaterRep_final_QE-HF_C18_USDAY63680_NEG_MSMS_75_ExCtrl_C_Rg80to1200-CE102040-soil-S1_Run209.h5"
 
-FROM python:3.8-slim-bullseye
+FROM python:3.11-slim-bullseye
 
 # This brings the above ARG values from the top of the file into this stage
 ARG BASE_DATA_URL

diff --git a/docker/local_jupyter.sh b/docker/local_jupyter.sh
@@ -5,7 +5,7 @@ set -euf -o pipefail
 SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 REPO_DIR=$(dirname "$SCRIPT_DIR")
 OUT_DIR="${SCRIPT_DIR}/out"
-IMAGE='ghcr.io/biorack/metatlas/metatlas_ci:1.2.0'
+IMAGE='ghcr.io/biorack/metatlas/metatlas_ci:1.3.0'
 PORT=8888
 
 while [[ "$#" -gt 0 ]]; do

diff --git a/docker/requirements.txt b/docker/requirements.txt
@@ -156,13 +156,13 @@ jsonschema-specifications==2023.7.1
     # via jsonschema
 jsonschema[format-nongpl]==4.19.1
     # via jsonschema
-jupyter-client==8.4.0
+jupyter-client==8.3.1
     # via
     #   -r requirements.in
     #   ipykernel
     #   jupyter-server
     #   nbclient
-jupyter-core==5.4.0
+jupyter-core==5.3.2
     # via
     #   ipykernel
     #   jupyter-client
@@ -175,15 +175,15 @@ jupyter-events==0.8.0
     # via jupyter-server
 jupyter-lsp==2.2.0
     # via jupyterlab
-jupyter-server==2.8.0
+jupyter-server==2.7.3
     # via
     #   jupyter-lsp
     #   jupyterlab
     #   jupyterlab-server
     #   notebook-shim
 jupyter-server-terminals==0.4.4
     # via jupyter-server
-jupyterlab==4.0.7
+jupyterlab==4.0.6
     # via -r requirements.in
 jupyterlab-pygments==0.2.2
     # via nbconvert

diff --git a/metatlas/plots/dill2plots.py b/metatlas/plots/dill2plots.py
@@ -652,8 +652,7 @@ def layout_rt_sliders(self):
 
     def create_radio_buttons(self, axes, labels, on_click_handler, radius, active_idx=0):
         buttons = RadioButtons(axes, labels, active=active_idx)
-        for circle in buttons.circles:
-            circle.set_radius(radius)
+        buttons.set_radio_props({'s':1600*radius, 'facecolor':'blue'})
         buttons.on_clicked(on_click_handler)
         return buttons
 
@@ -709,6 +708,11 @@ def on_motion(self, event):
                 self.mz_annot.set_visible(False)
                 self.fig.canvas.draw_idle()
 
+    def hide_radio_buttons(self):
+        self.peak_flag_radio.set_radio_props({'facecolor':'white'})
+        self.lin_log_radio.set_radio_props({'facecolor':'white'})
+        self.msms_flag_radio.set_radio_props({'facecolor':'white'})
+
     def update_plots(self):
         self.msms_zoom_factor = 1
         self.ax.cla()
@@ -717,6 +721,7 @@ def update_plots(self):
         self.rt_min_ax.cla()
         self.rt_max_ax.cla()
         self.y_scale_ax.cla()
+        self.hide_radio_buttons()
         self.set_plot_data()
 
     @log_errors(output_context=LOGGING_WIDGET)

diff --git a/tests/system/test_add_msms_ref.py b/tests/system/test_add_msms_ref.py
@@ -4,7 +4,7 @@
 
 
 def test_add_msms_ref_by_line01(tmp_path):
-    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.2.0"
+    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.3.0"
     expected = {}
     expected[
         str(tmp_path / "updated_refs.tab")

diff --git a/tests/system/test_c18.py b/tests/system/test_c18.py
@@ -4,7 +4,7 @@
 
 
 def test_c18_by_line01_with_remove(tmp_path):
-    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.2.0"
+    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.3.0"
     experiment = "20210915_JGI-AK_MK_506588_SoilWaterRep_final_QE-HF_C18_USDAY63680"
     expected = {}
     expected[

diff --git a/tests/system/test_hybrid.py b/tests/system/test_hybrid.py
@@ -4,7 +4,7 @@
 
 
 def test_hybrid_by_line01_with_remove(tmp_path):
-    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.2.0"
+    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.3.0"
     experiment = "20201106_JGI-AK_PS-KM_505892_OakGall_final_QE-HF_HILICZ_USHXG01583"
     expected = {}
     expected[

diff --git a/tests/system/test_rt_alignment.py b/tests/system/test_rt_alignment.py
@@ -6,7 +6,7 @@
 
 
 def test_rt_alignment_by_line01(tmp_path):
-    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.2.0"
+    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.3.0"
     experiment = "20201106_JGI-AK_PS-KM_505892_OakGall_final_QE-HF_HILICZ_USHXG01583"
     expected = {}
     expected[

diff --git a/tests/system/test_targeted.py b/tests/system/test_targeted.py
@@ -4,7 +4,7 @@
 
 
 def test_targeted_by_line01_with_remove(tmp_path):
-    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.2.0"
+    image = "ghcr.io/biorack/metatlas/metatlas_ci:1.3.0"
     experiment = "20201106_JGI-AK_PS-KM_505892_OakGall_final_QE-HF_HILICZ_USHXG01583"
     expected = {}
     expected[