spacr 0.9.23__tar.gz → 0.9.25__tar.gz

{spacr-0.9.23 → spacr-0.9.25}/MANIFEST.in

@@ -1,8 +1,6 @@
 recursive-include spacr/resources/models/cp *
 recursive-include spacr/resources/icons *
 recursive-include spacr/resources/font *
-recursive-include spacr/resources/MEDIAR *
-recursive-include spacr/resources/MEDIAR_weights *
 
 # Include essential files
 include *.py
@@ -31,14 +29,10 @@ global-exclude docs-env/
 
 # Exclude model files from distribution
 exclude spacr/resources/models/cp/*
-prune notebooks
-prune spacr/notebooks
+prune Notebooks
+prune spacr/Notebooks
 prune spacr/datasets
 
-# Exclude model files from distribution
-#exclude spacr/resources/models/cp/*
-#prune spacr/resources/models/cp
-
 # Exclude all notebooks (including old ones)
 prune notebooks
 prune spacr/notebooks

{spacr-0.9.23/spacr.egg-info → spacr-0.9.25}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.9.23
+Version: 0.9.25
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -118,7 +118,7 @@ Features
 -  **Sequencing:** Map FASTQ reads to barcode and gRNA barcode metadata.
 -  **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
 
-.. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v2.png
+.. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v3.png
    :alt: SpaCr workflow
    :align: center
 
@@ -167,7 +167,7 @@ Data Availability
 
 - **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
 
-- **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_
+- **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2076>`_
 
 Example Notebooks
 -----------------
@@ -200,5 +200,5 @@ See the `LICENSE <https://github.com/EinarOlafsson/spacr/blob/main/LICENSE>`_ fi
 How to Cite
 -----------
 If you use spaCR in your research, please cite:  
-Einar Olafsson, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
+Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
 

{spacr-0.9.23 → spacr-0.9.25}/README.rst

@@ -36,7 +36,7 @@ Features
 -  **Sequencing:** Map FASTQ reads to barcode and gRNA barcode metadata.
 -  **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
 
-.. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v2.png
+.. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v3.png
    :alt: SpaCr workflow
    :align: center
 
@@ -85,7 +85,7 @@ Data Availability
 
 - **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
 
-- **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_
+- **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2076>`_
 
 Example Notebooks
 -----------------
@@ -118,5 +118,5 @@ See the `LICENSE <https://github.com/EinarOlafsson/spacr/blob/main/LICENSE>`_ fi
 How to Cite
 -----------
 If you use spaCR in your research, please cite:  
-Einar Olafsson, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
+Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
 

{spacr-0.9.23 → spacr-0.9.25}/setup.py

@@ -71,7 +71,7 @@ dependencies = [
     'huggingface-hub>=0.24.0,<0.25'
 ]
 
-VERSION = "0.9.23"
+VERSION = "0.9.25"
 
 setup(
     name="spacr",

{spacr-0.9.23 → spacr-0.9.25}/spacr/gui_core.py

@@ -361,8 +361,8 @@ def setup_plot_section(vertical_container, settings_type):
     if settings_type == 'map_barcodes':
         current_dir = os.path.dirname(__file__)
         resources_path = os.path.join(current_dir, 'resources', 'icons')
-        gif_path = os.path.join(resources_path, 'dna_matrix.mp4')
-        display_media_in_plot_frame(gif_path, plot_frame)
+        #gif_path = os.path.join(resources_path, 'dna_matrix.mp4')
+        #display_media_in_plot_frame(gif_path, plot_frame)
 
         canvas = FigureCanvasTkAgg(figure, master=plot_frame)
         canvas.get_tk_widget().configure(cursor='arrow', highlightthickness=0)

{spacr-0.9.23 → spacr-0.9.25/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.9.23
+Version: 0.9.25
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -118,7 +118,7 @@ Features
 -  **Sequencing:** Map FASTQ reads to barcode and gRNA barcode metadata.
 -  **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
 
-.. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v2.png
+.. image:: https://github.com/EinarOlafsson/spacr/raw/main/spacr/resources/icons/flow_chart_v3.png
    :alt: SpaCr workflow
    :align: center
 
@@ -167,7 +167,7 @@ Data Availability
 
 - **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
 
-- **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_
+- **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2076>`_
 
 Example Notebooks
 -----------------
@@ -200,5 +200,5 @@ See the `LICENSE <https://github.com/EinarOlafsson/spacr/blob/main/LICENSE>`_ fi
 How to Cite
 -----------
 If you use spaCR in your research, please cite:  
-Einar Olafsson, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
+Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
 

{spacr-0.9.23 → spacr-0.9.25}/spacr.egg-info/SOURCES.txt

@@ -348,9 +348,8 @@ spacr/resources/icons/cellpose_masks.png
 spacr/resources/icons/classify.png
 spacr/resources/icons/convert.png
 spacr/resources/icons/default.png
-spacr/resources/icons/dna_matrix.mp4
 spacr/resources/icons/download.png
-spacr/resources/icons/flow_chart_v2.png
+spacr/resources/icons/flow_chart_v3.png
 spacr/resources/icons/logo.pdf
 spacr/resources/icons/logo_spacr.png
 spacr/resources/icons/logo_spacr_1.png
@@ -366,7 +365,4 @@ spacr/resources/icons/run.png
 spacr/resources/icons/sequencing.png
 spacr/resources/icons/settings.png
 spacr/resources/icons/train_cellpose.png
-spacr/resources/icons/umap.png
-spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif
-spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif
-spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif
+spacr/resources/icons/umap.png