create release 0.4.0

Author: davehorsfall

envs/build-docker-imgs.sh

@@ -1,5 +1,5 @@
 #! /bin/sh
-VERSION=0.3.2
+VERSION=0.4.0
 
 docker build --platform=linux/amd64 -t haniffalab/webatlas-pipeline:${VERSION} -f ./Dockerfile .
 docker build --platform=linux/amd64 -t haniffalab/webatlas-pipeline-build_config:${VERSION} -f ./Dockerfile.build_config .

main.nf

@@ -5,7 +5,7 @@ import groovy.json.*
 nextflow.enable.dsl=2
 
 verbose_log = true
-version = "0.3.2"
+version = "0.4.0"
 
 //////////////////////////////////////////////////////
 

multimodal.nf

@@ -9,7 +9,7 @@ nextflow.enable.dsl=2
 params.outdir = ""
 params.copy_raw = true
 
-version="0.3.2"
+version="0.4.0"
 verbose_log=true
 outdir_with_version = "${params.outdir.replaceFirst(/\/*$/, "")}\/${version}"
 

nextflow.config

@@ -13,9 +13,9 @@ profiles {
   docker { 
     docker.enabled = true
     process {
-      container = 'haniffalab/webatlas-pipeline:0.3.2'
+      container = 'haniffalab/webatlas-pipeline:0.4.0'
       withLabel: build_config {
-        container = 'haniffalab/webatlas-pipeline-build_config:0.3.2'
+        container = 'haniffalab/webatlas-pipeline-build_config:0.4.0'
       }
     }
   }

sphinx/citing.rst

@@ -11,4 +11,4 @@ Citation
 
 If you use this software in a scientific publication, please cite using the following Zenodo reference. 
 
-**Li, Tong, Horsfall, David, Basurto-Lozada, Daniela, Prete, Martin, Jessica, Cox, & Iolo, Squires. (2023). WebAtlas Pipeline (v0.3.2). Zenodo. https://doi.org/10.5281/zenodo.7863308**
+**Li, Tong, Horsfall, David, Basurto-Lozada, Daniela, Prete, Martin, Jessica, Cox, & Iolo, Squires. (2023). WebAtlas Pipeline (v0.4.0). Zenodo. https://doi.org/10.5281/zenodo.7863308**

sphinx/conf.py

@@ -23,7 +23,7 @@
 author = "Haniffa Lab"
 
 # The full version, including alpha/beta/rc tags
-release = "0.3.2"
+release = "0.4.0"
 
 # -- General configuration ---------------------------------------------------
 

sphinx/examples/visium.rst

@@ -99,7 +99,7 @@ verify the expected directories are created.
 .. code-block:: shell
    :caption: Input
 
-   ls -l output/CytAssist_FFPE_Human_Breast_Cancer/0.3.2
+   ls -l output/CytAssist_FFPE_Human_Breast_Cancer/0.4.0
 
 .. code-block:: shell
    :caption: Output
@@ -121,7 +121,7 @@ at http://localhost:3000, and that CORS is enabled via the Access-Control-Allow-
 .. code-block:: shell
    :caption: Input
 
-   npx http-server output/CytAssist_FFPE_Human_Breast_Cancer/0.3.2 --port 3000 --cors
+   npx http-server output/CytAssist_FFPE_Human_Breast_Cancer/0.4.0 --port 3000 --cors
 
 .. code-block:: shell
    :caption: Output

sphinx/examples/xenium.rst

@@ -102,7 +102,7 @@ verify the expected directories are created.
 .. code-block:: shell
    :caption: Input
 
-   ls -l output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.3.2
+   ls -l output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.4.0
 
 .. code-block:: shell
    :caption: Output
@@ -123,7 +123,7 @@ at http://localhost:3000, and that CORS is enabled via the Access-Control-Allow-
 .. code-block:: shell
    :caption: Input
 
-   npx http-server output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.3.2 --port 3000 --cors
+   npx http-server output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.4.0 --port 3000 --cors
 
 .. code-block:: shell
    :caption: Output

sphinx/installation.rst

@@ -14,43 +14,43 @@ Download the WebAtlas Pipeline release. You can look for previous `releases on G
 .. code-block:: shell
    :caption: Input
 
-   wget https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.3.2.tar.gz
+   wget https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.4.0.tar.gz
 
 .. code-block:: shell
    :caption: Expected Output
 
    Resolving github.com (github.com)... 140.82.121.3
    Connecting to github.com (github.com)|140.82.121.3|:443... connected.
    HTTP request sent, awaiting response... 302 Found
-   Location: https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.3.2 [following]
-   --2023-05-18 09:30:15--  https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.3.2
+   Location: https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.4.0 [following]
+   --2023-05-18 09:30:15--  https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.4.0
    Resolving codeload.github.com (codeload.github.com)... 140.82.121.9
    Connecting to codeload.github.com (codeload.github.com)|140.82.121.9|:443... connected.
    HTTP request sent, awaiting response... 200 OK
    Length: unspecified [application/x-gzip]
-   Saving to: ‘v0.3.2.tar.gz’
+   Saving to: ‘v0.4.0.tar.gz’
 
-   v0.3.2.tar.gz [ <=>                                           ]   2.70M  9.12MB/s    in 0.3s    
+   v0.4.0.tar.gz [ <=>                                           ]   2.70M  9.12MB/s    in 0.3s    
 
-   2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.3.2.tar.gz’ saved [2835534]
+   2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.4.0.tar.gz’ saved [2835534]
 
 Extract the WebAtlas compressed tag and change directory into the new repo.
 
 .. code-block:: shell
    :caption: Input
 
-   tar -xzvf ./v0.3.2.tar.gz
-   cd webatlas-pipeline-0.3.2
+   tar -xzvf ./v0.4.0.tar.gz
+   cd webatlas-pipeline-0.4.0
 
 .. code-block:: shell
    :caption: Expected Output
     
-   webatlas-pipeline-0.3.2/
-   webatlas-pipeline-0.3.2/.github/
+   webatlas-pipeline-0.4.0/
+   webatlas-pipeline-0.4.0/.github/
    ...
    ...
-   webatlas-pipeline-0.3.2/tests/input/simple_config.json
-   webatlas-pipeline-0.3.2/tests/test_class.py
+   webatlas-pipeline-0.4.0/tests/input/simple_config.json
+   webatlas-pipeline-0.4.0/tests/test_class.py
 
 .. _environment: