From 8cfb40230e226b7386ddeb37a707995977278a2b Mon Sep 17 00:00:00 2001 From: pdiakumis Date: Mon, 23 Mar 2026 00:45:03 +1100 Subject: [PATCH 1/3] change gh org --- .github/workflows/deploy.yaml | 10 +++++----- DESCRIPTION | 4 ++-- R/utils.R | 2 +- README.qmd | 20 ++++++++++---------- inst/documentation/installation/_r.qmd | 4 ++-- man/nemo-package.Rd | 6 +++--- pkgdown/_pkgdown.yml | 2 +- vignettes/NEWS.qmd | 2 +- vignettes/devnotes.qmd | 2 +- vignettes/structure.Rmd | 4 ++-- 10 files changed, 28 insertions(+), 28 deletions(-) diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index 7de451f..f9a54c2 100644 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -41,7 +41,7 @@ jobs: rattler-build build \ --channel umccr \ --channel conda-forge \ - --recipe ${conda_recipe}/recipe.yaml \ + --recipe ${{ env.conda_recipe }}/recipe.yaml \ --output-dir ${RUNNER_TEMP}/out1 - name: 🐍 Conda pkg upload run: | @@ -50,7 +50,7 @@ jobs: [[ "${{ github.ref }}" == "refs/heads/dev" ]] && LABEL_ARG="--channel dev" rattler-build upload anaconda \ --owner umccr \ - --api-key ${anaconda_token} \ + --api-key ${{ env.anaconda_token }} \ ${LABEL_ARG} \ ${pkg_path} - name: 🔒 Conda lock @@ -58,20 +58,20 @@ jobs: CHANNEL_ARGS="--channel umccr --channel conda-forge" [[ "${{ github.ref }}" == "refs/heads/dev" ]] && CHANNEL_ARGS="--channel umccr/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 diff --git a/DESCRIPTION b/DESCRIPTION index 72d6857..9596f3d 100644 --- a/DESCRIPTION +++ b/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) diff --git a/R/utils.R b/R/utils.R index 0a6d83e..e9fd331 100644 --- a/R/utils.R +++ b/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"), diff --git a/README.qmd b/README.qmd index 8c0b44b..ade1cae 100644 --- a/README.qmd +++ b/README.qmd @@ -22,20 +22,20 @@ use("nemo") options(width = 100) ``` -logo +logo # 🐢 Tidy and Explore Bioinformatic Pipeline Outputs [![conda-latest1]](https://anaconda.org/umccr/r-nemo) -[![gha]](https://github.com/umccr/nemo/actions/workflows/deploy.yaml) +[![gha]](https://github.com/tidywf/nemo/actions/workflows/deploy.yaml) [conda-latest1]: "Conda Latest Release" -[gha]: "GitHub Actions" +[gha]: "GitHub Actions" -- 📚 Docs: - - [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: + - [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 @@ -54,8 +54,8 @@ 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]: "tidywigits" -[dracarys]: "dracarys" +[tidywigits]: "tidywigits" +[dracarys]: "dracarys" ## 🍕 Installation @@ -65,7 +65,7 @@ Alternatively: - conda package: -For more details see: +For more details see: ## 🌀 CLI diff --git a/inst/documentation/installation/_r.qmd b/inst/documentation/installation/_r.qmd index 31064c1..73bf65b 100644 --- a/inst/documentation/installation/_r.qmd +++ b/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 ``` diff --git a/man/nemo-package.Rd b/man/nemo-package.Rd index 963632f..0ba508f 100644 --- a/man/nemo-package.Rd +++ b/man/nemo-package.Rd @@ -13,9 +13,9 @@ Provides the base components for tidying and exploring outputs from bioinformati \seealso{ Useful links: \itemize{ - \item \url{https://github.com/umccr/nemo} - \item \url{https://umccr.github.io/nemo/} - \item Report bugs at \url{https://github.com/umccr/nemo/issues} + \item \url{https://github.com/tidywf/nemo} + \item \url{https://tidywf.github.io/nemo/} + \item Report bugs at \url{https://github.com/tidywf/nemo/issues} } } diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index ba2b796..19e1a4e 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -1,4 +1,4 @@ -url: https://umccr.github.io/nemo +url: https://tidywf.github.io/nemo development: mode: auto title: nemo diff --git a/vignettes/NEWS.qmd b/vignettes/NEWS.qmd index 81e7402..b5b2f02 100644 --- a/vignettes/NEWS.qmd +++ b/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( diff --git a/vignettes/devnotes.qmd b/vignettes/devnotes.qmd index 78f6cab..525e687 100644 --- a/vignettes/devnotes.qmd +++ b/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 | diff --git a/vignettes/structure.Rmd b/vignettes/structure.Rmd index 78e0e42..7276c4a 100644 --- a/vignettes/structure.Rmd +++ b/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]: "R6 package repo" -[tidywigits]: "tidywigits" -[dracarys]: "dracarys" +[tidywigits]: "tidywigits" +[dracarys]: "dracarys" Here we use the `Tool1` and `Workflow1` classes as examples to illustrate the structure of the package. From 4bcdabdaad7a3546038e32e90f75c4d52d0587bb Mon Sep 17 00:00:00 2001 From: pdiakumis Date: Tue, 24 Mar 2026 17:17:44 +1100 Subject: [PATCH 2/3] change anaconda org --- CLAUDE.md | 2 +- README.qmd | 6 +++--- deploy/conda/env/yaml/nemo.yaml | 2 +- deploy/conda/env/yaml/pkgdown.yaml | 4 ++-- deploy/conda/recipe/recipe.yaml | 6 +++--- inst/documentation/installation/_conda.qmd | 12 ++++++------ inst/documentation/installation/_pixi.qmd | 2 +- inst/documentation/notes/pixi.md | 6 +++--- 8 files changed, 20 insertions(+), 20 deletions(-) diff --git a/CLAUDE.md b/CLAUDE.md index 03c4e0b..cd3d626 100644 --- a/CLAUDE.md +++ b/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)`) 5. Creates a git tag (`vVERSION`) — only on `main` diff --git a/README.qmd b/README.qmd index ade1cae..d9b1173 100644 --- a/README.qmd +++ b/README.qmd @@ -26,10 +26,10 @@ options(width = 100) # 🐢 Tidy and Explore Bioinformatic Pipeline Outputs -[![conda-latest1]](https://anaconda.org/umccr/r-nemo) +[![conda-latest1]](https://anaconda.org/tidywf/r-nemo) [![gha]](https://github.com/tidywf/nemo/actions/workflows/deploy.yaml) -[conda-latest1]: "Conda Latest Release" +[conda-latest1]: "Conda Latest Release" [gha]: "GitHub Actions" - 📚 Docs: @@ -63,7 +63,7 @@ for the _raw_ input _files_ and _tidy_ output _tbls_. Alternatively: -- conda package: +- conda package: For more details see: diff --git a/deploy/conda/env/yaml/nemo.yaml b/deploy/conda/env/yaml/nemo.yaml index 645b0d1..cf87a77 100644 --- a/deploy/conda/env/yaml/nemo.yaml +++ b/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 diff --git a/deploy/conda/env/yaml/pkgdown.yaml b/deploy/conda/env/yaml/pkgdown.yaml index 686b7ba..81d11d5 100644 --- a/deploy/conda/env/yaml/pkgdown.yaml +++ b/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 diff --git a/deploy/conda/recipe/recipe.yaml b/deploy/conda/recipe/recipe.yaml index cf24c7e..1dd4c14 100644 --- a/deploy/conda/recipe/recipe.yaml +++ b/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: diff --git a/inst/documentation/installation/_conda.qmd b/inst/documentation/installation/_conda.qmd index 3d2321d..0b6d8ac 100644 --- a/inst/documentation/installation/_conda.qmd +++ b/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]: "Conda package version" -[conda-latest]: "Conda package latest release date" +[conda-version]: "Conda package version" +[conda-latest]: "Conda package latest release date" -The conda package is available from the umccr channel at -. +The conda package is available from the tidywf channel at +. ```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 diff --git a/inst/documentation/installation/_pixi.qmd b/inst/documentation/installation/_pixi.qmd index 5062594..f1a8b95 100644 --- a/inst/documentation/installation/_pixi.qmd +++ b/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 ``` diff --git a/inst/documentation/notes/pixi.md b/inst/documentation/notes/pixi.md index 1b00107..d1a08bb 100644 --- a/inst/documentation/notes/pixi.md +++ b/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 "] -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. ``` From 54c90537d9374d12fe93e56240716006467fb27b Mon Sep 17 00:00:00 2001 From: pdiakumis Date: Tue, 24 Mar 2026 17:34:27 +1100 Subject: [PATCH 3/3] change anaconda org --- .github/workflows/deploy.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index f9a54c2..b959585 100644 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -39,7 +39,7 @@ jobs: - name: 🐍 Conda pkg build run: | rattler-build build \ - --channel umccr \ + --channel tidywf \ --channel conda-forge \ --recipe ${{ env.conda_recipe }}/recipe.yaml \ --output-dir ${RUNNER_TEMP}/out1 @@ -49,14 +49,14 @@ jobs: LABEL_ARG="" [[ "${{ github.ref }}" == "refs/heads/dev" ]] && LABEL_ARG="--channel dev" rattler-build upload anaconda \ - --owner umccr \ + --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 ${{ env.conda_env_yaml }}/${{ env.pkg_name }}.yaml \ ${CHANNEL_ARGS} \