Merge remote-tracking branch 'upstream/gating'

README.md

@@ -27,7 +27,8 @@ To import your imaging files in the import gui type in the mounted `/data/..`
 
 ## Clone and Run Codebase (for Developers)
 #### 1. Checkout Project
-`git clone https://github.com/labsyspharm/minerva_analysis.git`
+* `git clone https://github.com/labsyspharm/minerva_analysis.git`
+* `cd minerva_analysis`
 #### 2. Checkout Necessary Branch
 * **For Gating, run** `git checkout gating`
 * Run `git pull` to make sure everything is up to date 

package_mac.sh

@@ -1 +1 @@
-pyinstaller -F --paths $CONDA_PREFIX --add-data "minerva_analysis/client:minerva_analysis/client" --add-data "minerva_analysis/__init__.py:minerva_analysis/" --add-data "minerva_analysis/server:minerva_analysis/server" --add-data "$CONDA_PREFIX/lib/python3.9/site-packages/xmlschema/schemas:xmlschema/schemas" --add-data "$CONDA_PREFIX/lib/python3.9/site-packages/ome_types:ome_types" --hidden-import "scipy.spatial.transform._rotation_groups" --hidden-import "sqlalchemy.sql.default_comparator" --hidden-import "sklearn.neighbors._partition_nodes" --hidden-import "sklearn.neighbors.ball_tree" --hidden-import "sklearn.utils._typedefs" --hidden-import "cmath" --hidden-import "imagecodecs._shared" --hidden-import "imagecodecs._imcd" --name $1 run.py
+pyinstaller -F --paths $CONDA_PREFIX --add-data "minerva_analysis/client:minerva_analysis/client" --add-data "minerva_analysis/__init__.py:minerva_analysis/" --add-data "minerva_analysis/server:minerva_analysis/server" --add-data "$CONDA_PREFIX/lib/python3.9/site-packages/xmlschema/schemas:xmlschema/schemas" --add-data "$CONDA_PREFIX/lib/python3.9/site-packages/ome_types:ome_types"  --hidden-import "scipy.special._cdflib" --hidden-import "scipy.spatial.transform._rotation_groups" --hidden-import "sqlalchemy.sql.default_comparator" --hidden-import "sklearn.neighbors._partition_nodes" --hidden-import "sklearn.neighbors.ball_tree" --hidden-import "sklearn.utils._typedefs" --hidden-import "cmath" --hidden-import "imagecodecs._shared" --hidden-import "imagecodecs._imcd" --name $1 run.py

package_win.bat

@@ -1 +1 @@
-pyinstaller -F --paths $env:CONDA_PREFIX --add-data "minerva_analysis/client;minerva_analysis/client" --add-data "minerva_analysis/server;minerva_analysis/server" --add-data "%CONDA_PREFIX%/Lib/site-packages/xmlschema/schemas;xmlschema/schemas" --add-data "%CONDA_PREFIX%/Lib/site-packages/ome_types;ome_types" --hidden-import="scipy.spatial.transform._rotation_groups" --hidden-import="cmath" --hidden-import="sqlalchemy.sql.default_comparator" --hidden-import="sklearn.utils._typedefs" --hidden-import="sklearn.neighbors._partition_nodes" --hidden-import="sklearn.neighbors.ball_tree" --hidden-import="imagecodecs._shared" --hidden-import="imagecodecs._imcd" --icon icon.ico  --name minerva_analysis_windows run.py
+pyinstaller -F --paths $env:CONDA_PREFIX --add-data "minerva_analysis/client;minerva_analysis/client" --add-data "minerva_analysis/server;minerva_analysis/server" --add-data "%CONDA_PREFIX%/Lib/site-packages/xmlschema/schemas;xmlschema/schemas" --add-data "%CONDA_PREFIX%/Lib/site-packages/ome_types;ome_types" --hidden-import="scipy.special._cdflib" --hidden-import="scipy.spatial.transform._rotation_groups" --hidden-import="cmath" --hidden-import="sqlalchemy.sql.default_comparator" --hidden-import="sklearn.utils._typedefs" --hidden-import="sklearn.neighbors._partition_nodes" --hidden-import="sklearn.neighbors.ball_tree" --hidden-import="imagecodecs._shared" --hidden-import="imagecodecs._imcd" --icon icon.ico  --name minerva_analysis_windows run.py