Merge branch 'development' into no_upload_master

Author: ivansg44

.github/workflows/ci.yml

@@ -1,58 +1,53 @@
-# COVID-MVP
+# VIRUS-MVP
 
-SARS-CoV-2 lineages and variants pose high risk to global public health.
+Viral lineages and variants pose high risk to global public health.
 
-COVID-MVP is a heatmap-centric visualization web application that encodes
-mutational information across multiple SARS-CoV-2 lineages and variants. The
-data visualized by COVID-MVP is generated by two external projects:
+VIRUS-MVP is a heatmap-centric visualization web application that encodes
+mutational information across multiple groups, including SARS-CoV-2 lineages.
+The data visualized by VIRUS-MVP is generated by two external projects:
 
 * [nf-ncov-voc][nf-ncov-voc]
 * [Pokay][pokay]
 
-You can find a deployed version of this application (without user upload
-functionality) at [https://covidmvp.cidgoh.ca/][deployed].
-
-[deployed]: https://covidmvp.cidgoh.ca/
+You can find deployed versions of this application (without user upload
+functionality) at https://virusmvp.org/.
 
 ![app_interface]
 
 [app_interface]: screenshots/app_interface.png
 
 ## Installation
 
-### _0. (For users that plan to upload their own data)_ [Install Nextflow][nf]
+### _0. (If uploading your own data)_ Install [Nextflow][nf] & [Conda][conda].
 
 [nf]: https://www.nextflow.io/docs/latest/getstarted.html
+[conda]: https://conda.io/projects/conda/en/latest/user-guide/install/
 
 ### 1. Clone the repository and its submodules
 
-`$ git clone git@github.com:cidgoh/COVID-MVP.git --recurse-submodules`
+`$ git clone git@github.com:cidgoh/VIRUS-MVP.git --recurse-submodules`
 
 ### 2. Create a virtual environment
 
-We use [Conda][conda], but you can use [venv][venv]. We
-recommend using Python 3.9 in your virtual environment. Older Python versions
-may break the application.
-
-[conda]: https://docs.conda.io/en/latest/
-[venv]: https://docs.python.org/3/library/venv.html
+We use [Conda](https://docs.conda.io/en/latest/), but you can use
+[venv](https://docs.python.org/3/library/venv.html).
 
-`$ conda create --name=COVID-MVP python=3.9`
+`$ conda create --name=VIRUS-MVP`
 
 ### 3. Activate the environment
 
-`$ conda activate COVID-MVP`
+`$ conda activate VIRUS-MVP`
 
 ### 4. Install requirements
 
-`(COVID-MVP) $ pip install -r requirements.txt`
+`(VIRUS-MVP) $ pip install -r requirements.txt`
 
 ### 5. Run the application
 
 If you do not run the application from the root directory,
 some of the JavaScript assets will not be compiled.
 
-`(COVID-MVP) $ python app.py`
+`(VIRUS-MVP) $ python app.py`
 
 Go to http://0.0.0.0:8050/.
 
@@ -69,17 +64,15 @@ heatmap view.
 
 ### Heatmap view
 
-The left axis encodes SARS-CoV-2 lineages. Lineages belonging to VOC are in
+The left axis encodes viral lineages. Lineages belonging to VOC are in
 **bold**, and lineages belonging to VOI are in _italics_. Actively circulating
 lineages are denoted with ⚠️.
 
 The right axis encodes the number of genomic sequences analyzed for each
 lineage.
 
 The top axis encodes the nucleotide position of lineage mutations, with respect
-to the [reference SARS-CoV-2 genome][wuhan] from Wuhan.
-
-[wuhan]: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2
+to the reference genome.
 
 The bottom axis encodes the amino acid position of lineage mutations, in the
 following format:
@@ -138,14 +131,16 @@ corresponding to non-clade defining mutations.
 
 #### Uploading data
 
-The upload button ![upload_btn] allows you to upload your own SARs-CoV-2 genomic
-data in `FASTA` or `VCF` format.  You can find examples of files users can
-upload in [test_data/][3].
+The upload button ![upload_btn] allows you to upload your own genomic data in
+`FASTA` or `VCF` format.  You can find examples of files users can upload in
+[test_data/][3].
 
 [upload_btn]: screenshots/upload_btn.png
 [3]: test_data/
 
-_You must have Nextflow installed to upload files._
+_You must have Nextflow and Conda installed to upload files._
+
+_Your first upload will take a while. Subsequent uploads will be faster._
 
 #### Downloading data
 
@@ -158,11 +153,11 @@ examples of these reports in [surveillance_reports/][4].
 
 ## [nf-ncov-voc][nf-ncov-voc]
 
-Nextflow-wrapped workflow for SARS-CoV-2 variant calling.
+Nextflow-wrapped workflow for variant calling.
 
 ## [pokay][pokay]
 
-Repository for SARS-CoV-2 mutation functions.
+Repository for mutation functions.
 
 [nf-ncov-voc]: https://github.com/cidgoh/nf-ncov-voc/
 [pokay]: https://github.com/nodrogluap/pokay/

.github/workflows/submodule_update.yml

@@ -40,8 +40,8 @@
 # contains the visualization that is deployed by this file, when
 # ``app`` is served.
 app = dash.Dash(
-    name="COVID-MVP",
-    title="COVID-MVP",
+    name="VIRUS-MVP",
+    title="VIRUS-MVP",
     assets_folder=ASSETS_DIR,
     # We bring in jQuery for some of the JavaScript
     # callbacks.
@@ -813,9 +813,6 @@ def update_heatmap_sample_size_axis_fig(_, get_data_args, last_data_mtime):
 def update_heatmap_gene_bar_fig(_, get_data_args, last_data_mtime):
     """Update heatmap gene bar fig.
 
-    We need to update style because width might have changed due to
-    added nt positions in data.
-
     :param _: Heatmap cells fig updated
     :param get_data_args: Args for ``get_data``
     :type get_data_args: dict