From 212ff8c21d8bd4676a8c34e527fec0e9cae407bc Mon Sep 17 00:00:00 2001
From: jalew188 <jalew188@gmail.com>
Date: Tue, 26 Dec 2023 21:18:38 +0100
Subject: [PATCH] update installers

---
 alphaviz/gui.py                           |  4 ++--
 release/pyinstaller/alphaviz.spec         |  2 ++
 requirements/requirements.txt             |  5 +----
 requirements/requirements_development.txt | 10 +++-------
 requirements/requirements_gui.txt         |  7 ++-----
 5 files changed, 10 insertions(+), 18 deletions(-)

diff --git a/alphaviz/gui.py b/alphaviz/gui.py
index 3b9a8e8..fa75f1c 100644
--- a/alphaviz/gui.py
+++ b/alphaviz/gui.py
@@ -1066,7 +1066,7 @@ def display_chromatogram(self, *args):
             self.data.raw_data,
             self.colorscale_qualitative.value,
         )
-        chrom_widget = pn.Pane(
+        chrom_widget = pn.pane.panel(
             chromatograms,
             config=update_config('Chromatograms'),
             sizing_mode='stretch_width',
@@ -1230,7 +1230,7 @@ def run_after_protein_selection(self, *args):
                         self.curr_protein_ids = prot_id
                         break
 
-            self.layout[6] = pn.Pane(
+            self.layout[6] = pn.pane.panel(
                 self.protein_coverage_plot,
                 config=update_config(f"{self.gene_name}_coverage_plot"),
                 align='center',
diff --git a/release/pyinstaller/alphaviz.spec b/release/pyinstaller/alphaviz.spec
index f3b19f7..c88ed1b 100644
--- a/release/pyinstaller/alphaviz.spec
+++ b/release/pyinstaller/alphaviz.spec
@@ -97,6 +97,8 @@ for _pkg in ["python","accelerate"]:
 for _pkg in pkgs_to_check_at_runtime:
 	datas += copy_metadata(_pkg)
 
+datas += copy_metadata('datashader')
+
 a = Analysis(
 	[script_name],
 	pathex=[location],
diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index aa1a0ad..bcfe222 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -3,9 +3,6 @@ peptdeep
 alphabase
 alpharaw
 
-holoviews
 xarray
-dask
 multipledispatch
-plotly
-datashader
\ No newline at end of file
+plotly
\ No newline at end of file
diff --git a/requirements/requirements_development.txt b/requirements/requirements_development.txt
index f33e0db..80d6662 100644
--- a/requirements/requirements_development.txt
+++ b/requirements/requirements_development.txt
@@ -1,18 +1,14 @@
 jupyter==1.0.0
 jupyter_contrib_nbextensions==0.5.1
-pyinstaller
 autodocsumm==0.2.6
 sphinx-rtd-theme==0.5.2
 twine==3.4.1
-bumpversion
 pipdeptree==2.1.0
 ipykernel==6.4.0
+pytest==6.2.5
 tqdm
 psutil
-pytest==6.2.5
+bumpversion
+pyinstaller
 
 pywin32; sys_platform=='win32'
-
-alphatims
-peptdeep
-alphabase
diff --git a/requirements/requirements_gui.txt b/requirements/requirements_gui.txt
index d549aca..e197428 100644
--- a/requirements/requirements_gui.txt
+++ b/requirements/requirements_gui.txt
@@ -1,15 +1,12 @@
 bokeh==2.4.2
 matplotlib==3.4.3
+datashader==0.13.0
 holoviews==1.14.8
 panel==0.12.4
-pyteomics
+pyteomics==4.5
 plotly==5.8.0
 beautifulsoup4==4.10.0
 requests==2.27.1
 #selenium
 #chromedriver-binary
 jinja2==3.0.2
-
-alphatims
-peptdeep
-alphabase