🚚 Migrate to lamindb v1 (#136)

* No longer need to catch MissingContextUI from ln.track() * ✏️ Fix closing bracket * 👽️ Update package checks when creating records * 👽️ Adjust types in API tests * 👷 Add lamindb devel CI workflow * 📝 Remove UID from track in vignette * 📝 Update CHANGELOG and bump devel version * 🚸 Add check for Python lamindb version * 👷 Move lamindb devel check to main workflow * 👽️ Update opening TileDBSoma artifacts for v1 * 📌 Bump lamindb dependency to v1.0.2 --------- Co-authored-by: Luke Zappia <[email protected]>
laminlabs · Jan 20, 2025 · 3ebf151 · 3ebf151
1 parent 5634127
commit 3ebf151
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -23,6 +23,8 @@ jobs:
           - { os: ubuntu-latest, r: "devel", http-user-agent: "release", python: "3.x" }
           - { os: ubuntu-latest, r: "release", python: "3.x" }
           - { os: ubuntu-latest, r: "oldrel-1", python: "3.9" }
+          - { os: ubuntu-latest, r: "release", http-user-agent: "release", python: "3.x", lamin: "devel" }
+          - { os: ubuntu-latest, r: "devel", http-user-agent: "release", python: "3.x", lamin: "devel" }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -76,6 +78,10 @@ jobs:
       - name: Setup Python environment
         run: |
           laminr::install_lamindb(extra_packages = c("s3fs"))
+          if ("${{ matrix.config.lamin }}" == "devel") {
+            reticulate::use_virtualenv("r-lamindb")
+            reticulate::py_install("git+https://github.com/laminlabs/lamindb.git")
+          }
         shell: Rscript {0}
 
       - name: Log in to Lamin

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,13 @@
+# laminr devel
+
+## MAJOR CHANGES
+
+- Updates for compatibility with the Python `lamindb` v1.0 release
+
+## MINOR CHANGES
+
+- `db$track()` can not automatically create a transform UID when not supplied
+
 # laminr v0.3.1
 
 This release improves the UX for setting up the Python environment and adds functions to allow access to CLI functionality from R.
@@ -43,7 +53,6 @@ This release contains mostly UX improvements:
 - Update roadmap (PR #112).
 - Simplify `README` content (PR #116).
 
-
 # laminr v0.2.0
 
 This release adds support for creating new artifacts in a LaminDB instance.

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: laminr
 Title: Client for 'LaminDB'
-Version: 0.3.1
+Version: 0.3.1.9000
 Authors@R: c(
     person("Robrecht", "Cannoodt", email = "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3641-729X")),

diff --git a/R/Artifact.R b/R/Artifact.R
@@ -70,8 +70,7 @@ ArtifactRecord <- R6::R6Class( # nolint object_name_linter
     #' @return A [tiledbsoma::SOMACollection] or [tiledbsoma::SOMAExperiment]
     #' object
     open = function() {
-      is_tiledbsoma <- private$get_value("suffix") == ".tiledbsoma" ||
-        private$get_value("_accessor") == "tiledbsoma"
+      is_tiledbsoma <- private$get_value("otype") == "tiledbsoma"
 
       if (!is_tiledbsoma) {
         cli::cli_abort(

diff --git a/R/Instance.R b/R/Instance.R
@@ -74,6 +74,22 @@ create_instance <- function(instance_settings, is_default = FALSE) {
     }
   )
 
+  if (!is.null(py_lamin)) {
+    lamin_version <- reticulate::py_get_attr(py_lamin, "__version__")
+    lamin_version_clean <- sub("([a-zA-Z].*)", "", lamin_version) # Remove pre-release versions, e.g. 1.0a5 -> 1.0
+    if (compareVersion("1.0.2", lamin_version_clean) == 1) {
+      cli::cli_abort(
+        c(
+          paste(
+            "This version of {.pkg laminr} requires Python {.pkg lamindb} >= 1.0.",
+            "You have {.pkg lamindb} v{lamin_version}."
+          ),
+          "i" = "Run {.run laminr::install_lamindb()} to update."
+        )
+      )
+    }
+  }
+
   # create the instance
   RichInstance$new(
     settings = instance_settings,
@@ -229,34 +245,7 @@ Instance <- R6::R6Class( # nolint object_name_linter
         }
       }
 
-      if (is.null(transform)) {
-        transform <- tryCatch(
-          py_lamin$track(path = path),
-          error = function(err) {
-            py_err <- reticulate::py_last_error()
-            # please don't change the below without changing it in lamindb
-            if (py_err$type != "MissingContextUID") {
-              cli::cli_abort(c(
-                "Python {py_err$message}",
-                "i" = "Run {.run reticulate::py_last_error()} for details"
-              ))
-            }
-
-            uid <- gsub(".*\\(\"(.*?)\"\\).*", "\\1", py_err$value)
-            cli::cli_inform(paste(
-              "To track this notebook, run: db$track(\"{uid}\")"
-            ))
-          }
-        )
-      } else {
-        if (is.character(transform) && nchar(transform) != 16) {
-          cli::cli_abort(
-            "The transform UID must be exactly 16 characters, got {nchar(transform)}"
-          )
-        }
-
-        py_lamin$track(transform = transform, path = path)
-      }
+      py_lamin$track(transform = transform, path = path)
     },
     #' @description Finish a tracked run
     finish = function() {

diff --git a/R/Registry.R b/R/Registry.R
@@ -519,7 +519,7 @@ create_record_from_python <- function(py_record, instance) {
 
   class_split <- strsplit(py_classes[1], "\\.")[[1]]
   module_name <- class_split[1]
-  if (module_name == "lnschema_core") {
+  if (module_name == "lamindb") {
     module_name <- "core"
   }
   registry_name <- tolower(class_split[3])
@@ -534,7 +534,7 @@ create_record_from_python <- function(py_record, instance) {
         NULL
       }
     )
-    if (inherits(value, "lnschema_core.models.Record")) {
+    if (inherits(value, "lamindb.models.Record")) {
       value <- create_record_from_python(value, instance)
     }
     value

diff --git a/R/install.R b/R/install.R
@@ -35,7 +35,7 @@ install_lamindb <- function(..., envname = "r-lamindb", extra_packages = NULL,
     reticulate::virtualenv_remove(envname)
   }
 
-  packages <- unique(c("lamindb", "ipython", extra_packages))
+  packages <- unique(c("lamindb>=1.0.2", "ipython", extra_packages))
 
   reticulate::py_install(packages = packages, envname = envname, ...)
 

diff --git a/tests/testthat/test-instance_api.R b/tests/testthat/test-instance_api.R
@@ -52,7 +52,7 @@ test_that("get_record works", {
   # try to get a record
   artifact <- api$get_record("core", "artifact", "mePviem4DGM4SFzvLXf3")
 
-  expect_true(all(c("uid", "size", "hash", "description", "type") %in% names(artifact)))
+  expect_true(all(c("uid", "size", "hash", "description") %in% names(artifact)))
 })
 
 test_that("test get_record fails gracefully with incorrect host", {
@@ -78,7 +78,7 @@ test_that("get_record with select works", {
   # try to get a record
   artifact <- api$get_record("core", "artifact", "mePviem4DGM4SFzvLXf3", select = "storage")
 
-  expect_true(all(c("uid", "size", "hash", "description", "type") %in% names(artifact)))
+  expect_true(all(c("uid", "size", "hash", "description") %in% names(artifact)))
 
   expect_true(all(c("uid", "type", "region", "root") %in% names(artifact$storage)))
 })

diff --git a/vignettes/laminr.Rmd b/vignettes/laminr.Rmd
@@ -65,15 +65,9 @@ LaminDB tracks which code is used to create data.
 To track the current source code, run:
 
 ```{r track, eval = submit_eval}
-db$track("I8BlHXFXqZOG0000")
+db$track()
 ```
 
-<div class="alert alert-info" role="alert">
-**Tip**
-
-The UID (here `"I8BlHXFXqZOG0000"`) is obtained by running `db$track()` and copying the UID from the output.
-</div>
-
 # Connect to other instances
 
 It is possible to connect to any LaminDB instance for reading data.