Change GitHub + Anaconda orgs

.github/workflows/deploy.yaml

@@ -39,39 +39,39 @@ jobs:
       - name: 🐍 Conda pkg build
         run: |
           rattler-build build \
-            --channel umccr \
+            --channel tidywf \
             --channel conda-forge \
-            --recipe ${conda_recipe}/recipe.yaml \
+            --recipe ${{ env.conda_recipe }}/recipe.yaml \
             --output-dir ${RUNNER_TEMP}/out1
       - name: 🐍 Conda pkg upload
         run: |
           pkg_path=$(find ${RUNNER_TEMP}/out1 -type f -name "*.conda")
           LABEL_ARG=""
           [[ "${{ github.ref }}" == "refs/heads/dev" ]] && LABEL_ARG="--channel dev"
           rattler-build upload anaconda \
-            --owner umccr \
-            --api-key ${anaconda_token} \
+            --owner tidywf \
+            --api-key ${{ env.anaconda_token }} \
             ${LABEL_ARG} \
             ${pkg_path}
       - name: 🔒 Conda lock
         run: |
-          CHANNEL_ARGS="--channel umccr --channel conda-forge"
-          [[ "${{ github.ref }}" == "refs/heads/dev" ]] && CHANNEL_ARGS="--channel umccr/label/dev ${CHANNEL_ARGS}"
+          CHANNEL_ARGS="--channel tidywf --channel conda-forge"
+          [[ "${{ github.ref }}" == "refs/heads/dev" ]] && CHANNEL_ARGS="--channel tidywf/label/dev ${CHANNEL_ARGS}"
           conda-lock lock \
-            --file ${conda_env_yaml}/${pkg_name}.yaml \
+            --file ${{ env.conda_env_yaml }}/${{ env.pkg_name }}.yaml \
             ${CHANNEL_ARGS} \
             -p linux-64
           conda-lock render \
             -p linux-64 \
             conda-lock.yml \
           && rm conda-lock.yml \
-          && mv conda-linux-64.lock ${conda_env_lock}/
+          && mv conda-linux-64.lock ${{ env.conda_env_lock }}/
       - name: 💾 Commit lockfiles
         run: |
           git status
           git config --local user.email "actions@github.com"
           git config --local user.name "GitHub Actions"
-          MSG="[bot] Updating conda-lock files (v${VERSION})"
+          MSG="[bot] Updating conda-lock files (v${{ env.VERSION }})"
           git add .
           git commit -m "${MSG}"
           git push

CLAUDE.md

@@ -137,7 +137,7 @@ The `conda-docs` workflow triggers on pushes to `main` or `dev`, but only runs w
 
 **`conda`** — builds and uploads the conda package:
 1. Builds the package with `rattler-build` using the recipe at `deploy/conda/recipe/recipe.yaml`
-2. Uploads to Anaconda under the `umccr` owner; uses `--channel dev` label when on the `dev` branch
+2. Uploads to Anaconda under the `tidywf` owner; uses `--channel dev` label when on the `dev` branch
 3. Regenerates the conda lock file (`deploy/conda/env/lock/conda-linux-64.lock`) for `linux-64`
 4. Commits and pushes the updated lock file as a bot commit (`[bot] Updating conda-lock files (v<VERSION>)`)
 5. Creates a git tag (`vVERSION`) — only on `main`

DESCRIPTION

@@ -10,8 +10,8 @@ Authors@R:
            email = "peterdiakumis@gmail.com",
            comment = c(ORCID = "0000-0002-7502-7545"))
      )
-URL: https://github.com/umccr/nemo, https://umccr.github.io/nemo/
-BugReports: https://github.com/umccr/nemo/issues
+URL: https://github.com/tidywf/nemo, https://tidywf.github.io/nemo/
+BugReports: https://github.com/tidywf/nemo/issues
 License: MIT + file LICENSE
 Depends:
     R (>= 4.4)

R/utils.R

@@ -204,7 +204,7 @@ get_python <- function() {
 nemoverse_wf_dispatch <- function(wf = NULL) {
   stopifnot(!is.null(wf))
   wfs <- list(
-    wigits = list(pkg = "tidywigits", wf = "Wigits", repo = "https://github.com/umccr/tidywigits"),
+    wigits = list(pkg = "tidywigits", wf = "Wigits", repo = "https://github.com/tidywf/tidywigits"),
     basemean = list(pkg = "base", wf = "mean", repo = "CRAN"),
     dummy1 = list(pkg = "dummy1", wf = "bar", repo = "BAZ")
     # dragen = list(pkg = "dracarys", wf = "Dragen"),

README.qmd

@@ -22,20 +22,20 @@ use("nemo")
 options(width = 100)
 ```
 
-<a href="https://umccr.github.io/nemo"><img src="man/figures/logo.png" alt="logo" align="left" height="100" /></a>
+<a href="https://tidywf.github.io/nemo"><img src="man/figures/logo.png" alt="logo" align="left" height="100" /></a>
 
 # 🐢 Tidy and Explore Bioinformatic Pipeline Outputs
 
-[![conda-latest1]](https://anaconda.org/umccr/r-nemo)
-[![gha]](https://github.com/umccr/nemo/actions/workflows/deploy.yaml)
+[![conda-latest1]](https://anaconda.org/tidywf/r-nemo)
+[![gha]](https://github.com/tidywf/nemo/actions/workflows/deploy.yaml)
 
-[conda-latest1]: <https://anaconda.org/umccr/r-nemo/badges/latest_release_date.svg> "Conda Latest Release"
-[gha]: <https://github.com/umccr/nemo/actions/workflows/deploy.yaml/badge.svg> "GitHub Actions"
+[conda-latest1]: <https://anaconda.org/tidywf/r-nemo/badges/latest_release_date.svg> "Conda Latest Release"
+[gha]: <https://github.com/tidywf/nemo/actions/workflows/deploy.yaml/badge.svg> "GitHub Actions"
 
-- 📚 Docs: <https://umccr.github.io/nemo>
-  - [Installation](https://umccr.github.io/nemo/articles/installation)
-  - [R6 structure](https://umccr.github.io/nemo/articles/structure)
-  - [Changelog](https://umccr.github.io/nemo/articles/NEWS)
+- 📚 Docs: <https://tidywf.github.io/nemo>
+  - [Installation](https://tidywf.github.io/nemo/articles/installation)
+  - [R6 structure](https://tidywf.github.io/nemo/articles/structure)
+  - [Changelog](https://tidywf.github.io/nemo/articles/NEWS)
 
 ## Overview
 
@@ -54,18 +54,18 @@ in YAML that are part of 'child' {nemo} packages, like {[tidywigits]} and
 packages) specify the schemas, types, patterns and field descriptions
 for the _raw_ input _files_ and _tidy_ output _tbls_.
 
-[tidywigits]: <https://github.com/umccr/tidywigits> "tidywigits"
-[dracarys]: <https://github.com/umccr/dracarys> "dracarys"
+[tidywigits]: <https://github.com/tidywf/tidywigits> "tidywigits"
+[dracarys]: <https://github.com/tidywf/dracarys> "dracarys"
 
 ## 🍕 Installation
 
 {{< include /inst/documentation/installation/_r.qmd >}}
 
 Alternatively:
 
-- conda package: <https://anaconda.org/umccr/r-nemo>
+- conda package: <https://anaconda.org/tidywf/r-nemo>
 
-For more details see: <https://umccr.github.io/nemo/articles/installation>
+For more details see: <https://tidywf.github.io/nemo/articles/installation>
 
 ## 🌀 CLI
 

deploy/conda/env/yaml/nemo.yaml

@@ -1,6 +1,6 @@
 name: nemo_env
 channels:
-  - umccr
+  - tidywf
   - conda-forge
 dependencies:
   - r-nemo ==0.0.3.9006 # bump

deploy/conda/env/yaml/pkgdown.yaml

@@ -1,7 +1,7 @@
 name: pkgdown_env
 channels:
-  - umccr/label/dev
-  - umccr
+  - tidywf/label/dev
+  - tidywf
   - conda-forge
 dependencies:
   - r-nemo ==0.0.3.9006 # bump

deploy/conda/recipe/recipe.yaml

@@ -64,13 +64,13 @@ tests:
     - nemo.R --version
 
 about:
-  homepage: https://github.com/umccr/nemo
+  homepage: https://github.com/tidywf/nemo
   summary: Tidy and explore outputs from bioinformatic pipelines
   description: Provides the building blocks for tidying and exploring outputs from bioinformatic pipelines.
   license: MIT
   license_file: LICENSE
-  repository: https://github.com/umccr/nemo
-  documentation: https://umccr.github.io/nemo
+  repository: https://github.com/tidywf/nemo
+  documentation: https://tidywf.github.io/nemo
 
 extra:
   recipe-maintainers:

inst/documentation/installation/_conda.qmd

@@ -1,15 +1,15 @@
-[![conda-version] ![conda-latest]](https://anaconda.org/umccr/r-nemo)
+[![conda-version] ![conda-latest]](https://anaconda.org/tidywf/r-nemo)
 
-[conda-version]: <https://anaconda.org/umccr/r-nemo/badges/version.svg> "Conda package version"
-[conda-latest]: <https://anaconda.org/umccr/r-nemo/badges/latest_release_date.svg> "Conda package latest release date"
+[conda-version]: <https://anaconda.org/tidywf/r-nemo/badges/version.svg> "Conda package version"
+[conda-latest]: <https://anaconda.org/tidywf/r-nemo/badges/latest_release_date.svg> "Conda package latest release date"
 
-The conda package is available from the umccr channel at
-<https://anaconda.org/umccr/r-nemo>.
+The conda package is available from the tidywf channel at
+<https://anaconda.org/tidywf/r-nemo>.
 
 ```bash
 conda create \
   -n nemo_env \
-  -c umccr -c conda-forge \
+  -c tidywf -c conda-forge \
   r-nemo==0.0.3.9006
 
 conda activate nemo_env

inst/documentation/installation/_pixi.qmd

@@ -2,7 +2,7 @@ If you use [Pixi](https://pixi.sh/), you can create a new isolated environment
 with the deployed conda package:
 
 ```bash
-pixi init -c umccr -c conda-forge ./tidy_env
+pixi init -c tidywf -c conda-forge ./tidy_env
 cd ./tidy_env
 pixi add r-nemo==0.0.3.9006
 ```

inst/documentation/installation/_r.qmd

@@ -2,6 +2,6 @@ Using {remotes} directly from GitHub:
 
 ```r
 install.packages("remotes")
-remotes::install_github("umccr/nemo") # latest main commit
-remotes::install_github("umccr/nemo@v0.0.3.9006") # released version
+remotes::install_github("tidywf/nemo") # latest main commit
+remotes::install_github("tidywf/nemo@v0.0.3.9006") # released version
 ```

inst/documentation/notes/pixi.md

@@ -10,7 +10,7 @@ brew install pixi
 
 ```
 cd my_projects
-pixi init hello-world -c conda-forge -c umccr
+pixi init hello-world -c conda-forge -c tidywf
 cd hello-world
 ```
 
@@ -21,7 +21,7 @@ A TOML file `pixi.toml` is created in the project directory:
 ```toml
 [workspace]
 authors = ["pdiakumis <peterdiakumis@gmail.com>"]
-channels = ["conda-forge", "umccr"]
+channels = ["conda-forge", "tidywf"]
 name = "hello-world"
 platforms = ["osx-arm64"]
 version = "0.1.0"
@@ -35,7 +35,7 @@ version = "0.1.0"
 
 - dependencies
 
-This will look into the `conda-forge` and `umccr` conda channels for `r-tidywigits`,
+This will look into the `conda-forge` and `tidywf` conda channels for `r-tidywigits`,
 and install it into `./.pixi` along with its dependencies.
 
 ```

pkgdown/_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://umccr.github.io/nemo
+url: https://tidywf.github.io/nemo
 development:
   mode: auto
 title: nemo

vignettes/NEWS.qmd

@@ -22,7 +22,7 @@ knitr:
 ```
 
 ```{r echo=FALSE}
-repo <- "https://github.com/umccr/nemo"
+repo <- "https://github.com/tidywf/nemo"
 vdiff <- function(new, old) {
   stopifnot(utils::compareVersion(new, old) == 1)
   htmltools::a(

vignettes/devnotes.qmd

@@ -64,7 +64,7 @@ remote storage and allow these processes to take place.
 | `dvc remote modify my_r2 endpointurl https://<...>.r2.cloudflarestorage.com` | add Cloudflare R2 remote endpointurl    |
 | `dvc remote list`                                                            | list all remotes                        |
 | `dvc check-ignore *`                                                         | check what is dvc-ignored               |
-| `dvc list https://github.com/umccr/tidywigits inst/extdata`                  | list dvc'ed data                        |
+| `dvc list https://github.com/tidywf/tidywigits inst/extdata`                  | list dvc'ed data                        |
 | `dvc add path/to/folder`                                                     | adds `folder` (and its contents) to dvc |
 | `dvc add path/to/file.txt`                                                   | adds `file.txt` to dvc                  |
 | `dvc push`                                                                   | pushes dvc data to remote               |

vignettes/structure.Rmd

@@ -70,8 +70,8 @@ the {nemo} parent classes. This allows for custom parsers and tidiers for specif
 bioinformatic tools and workflows.
 
 [R6]: <https://github.com/r-lib/R6> "R6 package repo"
-[tidywigits]: <https://github.com/umccr/tidywigits> "tidywigits"
-[dracarys]: <https://github.com/umccr/dracarys> "dracarys"
+[tidywigits]: <https://github.com/tidywf/tidywigits> "tidywigits"
+[dracarys]: <https://github.com/tidywf/dracarys> "dracarys"
 
 Here we use the `Tool1` and `Workflow1` classes as examples to illustrate the
 structure of the package.