🐛 Fix CI setup (#125)

* fix lamindb installation instructions * remove huggingface_hub * simplify installation instructions * manually set python * install python first * fix ga * remove env * no need to install bionty and wetlab during r cmd check * add which * set reticulate_python * check r installation dependencies * update error message * add debug vignette * fix style * do not reinstall tiledbsoma if already installed * add workaround * fix warning message * fix warning * add message * use smaller example dataset * revert debugging code * move lamindb installation to where it was before * align ci yamls * laminr is not installed yet at this stage * fix ci
laminlabs · Dec 3, 2024 · f5bd317 · f5bd317
1 parent f4b103a
commit f5bd317
Show file tree

Hide file tree

Showing 7 changed files with 63 additions and 31 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -40,8 +40,6 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-tinytex@v2
-
       - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.config.python }}
@@ -62,6 +60,11 @@ jobs:
           echo "LDFLAGS=-L$OPENBLAS/lib" >> $GITHUB_ENV
           echo "CPPFLAGS=-I$OPENBLAS/include" >> $GITHUB_ENV
 
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
       - name: Install {tiledbsoma}
         if: runner.os == 'Linux'
         run: |
@@ -71,7 +74,11 @@ jobs:
 
       - name: Install lamindb
         run: |
-          pip install 'lamindb[aws]>=0.77.2' huggingface_hub
+          pip install 'lamindb[aws]>=0.77.2'
+
+          # Make sure IPython is installed --
+          # Workaround for laminlabs/laminhub-public#29
+          pip install ipython
 
       - name: Log in to Lamin
         run: |
@@ -81,12 +88,21 @@ jobs:
         run: |
           lamin connect laminlabs/lamindata
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::rcmdcheck
-          needs: check
+      - name: Check whether we can import lamindb and connect to the default instance
+        run: |
+          reticulate::py_config()
+          reticulate::import("lamindb")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
 
-      - uses: r-lib/actions/check-r-package@v2
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
         with:
-          upload-snapshots: true
-          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -31,6 +31,10 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
@@ -41,15 +45,24 @@ jobs:
           needs: website
           quarto-version: pre-release
 
-      - name: Install {tiledbsoma}
+      - name: Install {tiledbsoma} if not already installed
         run: |
-          options(repos = c("https://chanzuckerberg.r-universe.dev", getOption("repos")))
-          install.packages("tiledbsoma")
+          if (!requireNamespace("tiledbsoma", quietly = TRUE)) {
+            options(repos = c("https://chanzuckerberg.r-universe.dev", getOption("repos")))
+            install.packages("tiledbsoma")
+          } else {
+            message("Package 'tiledbsoma' already installed")
+          }
         shell: Rscript {0}
 
       - name: Install lamindb
         run: |
-          pip install 'lamindb[aws]>=0.77.2' huggingface_hub
+          # install bionty and wetlab to avoid warnings about missing dependencies
+          pip install 'lamindb[aws,bionty,wetlab]>=0.77.2'
+
+          # Make sure IPython is installed --
+          # Workaround for laminlabs/laminhub-public#29
+          pip install ipython
 
       - name: Log in to Lamin
         run: |
@@ -59,6 +72,13 @@ jobs:
         run: |
           lamin connect laminlabs/lamindata
 
+      - name: Check whether we can import lamindb and connect to the default instance
+        run: |
+          reticulate::py_config()
+          reticulate::import("lamindb")
+          laminr::connect()
+        shell: Rscript {0}
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}

diff --git a/R/Artifact.R b/R/Artifact.R
@@ -27,7 +27,6 @@ ArtifactRecord <- R6::R6Class( # nolint object_name_linter
     #'
     #' @return The path to the cached artifact
     cache = function() {
-
       py_lamin <- private$.instance$get_py_lamin()
       if (!is.null(py_lamin)) {
         if (isTRUE(private$.instance$is_default)) {

diff --git a/R/Instance.R b/R/Instance.R
@@ -59,23 +59,20 @@ create_instance <- function(instance_settings, is_default = FALSE) {
     active = active
   )
 
-  py_lamin <- NULL
   check_requires("Connecting to Python", "reticulate", alert = "warning")
   py_lamin <- tryCatch(
     reticulate::import("lamindb"),
     error = function(err) {
+      cli::cli_warn(c(
+        paste(
+          "Failed to connect to the Python {.pkg lamindb} package,",
+          "some functionality may be limited."
+        ),
+        "i" = "Run {.run reticulate::py_config()} and {.run reticulate::py_last_error()} for details"
+      ))
       NULL
     }
   )
-  if (isTRUE(is_default) && is.null(py_lamin)) {
-    cli::cli_warn(c(
-      paste(
-        "Default instance failed to connect to the Python {.pkg lamindb} package,",
-        "you will not be able to create records"
-      ),
-      "i" = "See {.run reticulate::py_config()} for more information"
-    ))
-  }
 
   # create the instance
   RichInstance$new(
@@ -107,7 +104,7 @@ create_instance <- function(instance_settings, is_default = FALSE) {
 #' db <- connect("laminlabs/cellxgene")
 #'
 #' # fetch an artifact
-#' artifact <- db$Artifact$get("KBW89Mf7IGcekja2hADu")
+#' artifact <- db$Artifact$get("MkRm3eUKPwfnAyZMWD9v")
 #'
 #' # describe the artifact
 #' artifact$describe()

diff --git a/man/Instance.Rd b/man/Instance.Rd
diff --git a/vignettes/architecture.qmd b/vignettes/architecture.qmd
@@ -230,7 +230,7 @@ For example, to get an artifact with a specific ID using **only** base classes,
 ```r
 db <- connect("laminlabs/cellxgene")
 
-artifact <- db$get_module("core")$get_registry("artifact")$get("KBW89Mf7IGcekja2hADu")
+artifact <- db$get_module("core")$get_registry("artifact")$get("MkRm3eUKPwfnAyZMWD9v")
 
 artifact$get_value("id")
 ```
@@ -240,7 +240,7 @@ With the sugar syntax classes, you can achieve the same result more concisely:
 ```r
 db <- connect("laminlabs/cellxgene")
 
-artifact <- db$Artifact$get("KBW89Mf7IGcekja2hADu")
+artifact <- db$Artifact$get("MkRm3eUKPwfnAyZMWD9v")
 
 artifact$id
 ```

diff --git a/vignettes/concepts_features.Rmd b/vignettes/concepts_features.Rmd
@@ -109,10 +109,10 @@ db$Artifact$df(limit = 5)
 
 ## Working with records
 
-You can fetch a specific record from a registry using its ID or UID. For instance, to get the artifact with UID [KBW89Mf7IGcekja2hADu](https://lamin.ai/laminlabs/cellxgene/artifact/KBW89Mf7IGcekja2hADu):
+You can fetch a specific record from a registry using its ID or UID. For instance, to get the artifact with UID [MkRm3eUKPwfnAyZMWD9v](https://lamin.ai/laminlabs/cellxgene/artifact/MkRm3eUKPwfnAyZMWD9v):
 
 ```{r get_artifact}
-artifact <- db$Artifact$get("KBW89Mf7IGcekja2hADu")
+artifact <- db$Artifact$get("MkRm3eUKPwfnAyZMWD9v")
 ```
 
 This artifact contains an `AnnData` object with myeloid cell data. You can view its metadata: