fix: merge in master

latchbio · Dec 14, 2024 · b649237 · b649237
2 parents 1d47d50 + f29f295
commit b649237
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Showing 9 changed files with 425 additions and 389 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,7 +16,7 @@ Types of changes
 
 # Latch SDK Changelog
 
-## 2.55.1 - 2024-12-13
+## 2.55.1 - 2024-12-14
 
 ### Added
 
@@ -26,9 +26,23 @@ Types of changes
 
 * Update latch base image to 'cb01-main'
 
+## 2.55.0 - 2024-12-13
+
+### Changed
+
+* `latch dockerfile` now accepts explicit options for files containing
+  * apt deps
+  * conda deps
+  * r deps
+  * pip deps
+  * pyproject.toml / setup.py
+  * .env
+* `latch dockerfile` no longer does implicit dependency inferrence based on the presence of special files in the project root directory - now all dependency files need to be passed explicitly in the command line.
+
+
 ## 2.54.10 - 2024-12-06
 
-### Updated
+### Changed
 
 * Bump ephemeral storage limits for V100 GPU pods
 
@@ -46,7 +60,7 @@ Types of changes
 
 ## 2.54.7 - 2024-12-02
 
-### Updated
+### Changed
 
 * Add more ephemeral storage to large GPU pods
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -170,6 +170,9 @@ ignore = [
 
   "ANN101",
   "ANN102",
+  "ANN201",
+  "ANN202",
+  "ANN204",
 
   "E402",
   "E501",
@@ -178,10 +181,11 @@ ignore = [
   "C408",
   "C901",
 
+  "FA100",
+
   "T201",
   "T203",
 
-  "D415",
 
   "SIM108",
 
@@ -198,6 +202,8 @@ ignore = [
   "D105",
   "D106",
   "D107",
+  "D202",
+  "D415",
 
   "TRY003",
   "TRY300",
@@ -207,6 +213,8 @@ ignore = [
 
   "PERF203",
 
+  "PLC0415",
+
   "PLW2901",
   "PLW0603",
 
@@ -229,6 +237,7 @@ ignore = [
 
   "PD901",
 
+  "UP006",
   "UP040",
 
   "SIM112",

diff --git a/src/latch_cli/centromere/ctx.py b/src/latch_cli/centromere/ctx.py
@@ -40,6 +40,7 @@ class _Container:
     image_name: str
 
 
+# todo(ayush): cleanse this
 class _CentromereCtx:
     """Manages state for interaction with centromere.
 
@@ -270,8 +271,7 @@ def __init__(
                         )
                         click.secho(f"`{new_meta}`", bold=True, fg="red", nl=False)
                         click.secho(
-                            f" file:\n```\n{snakemake_metadata_example}```",
-                            fg="red",
+                            f" file:\n```\n{snakemake_metadata_example}```", fg="red"
                         )
                         if click.confirm(
                             click.style(
@@ -299,9 +299,10 @@ def __init__(
                                 import subprocess
 
                                 if system == "Linux":
-                                    res = subprocess.run(
-                                        ["xdg-open", new_meta]
-                                    ).returncode
+                                    res = subprocess.run([
+                                        "xdg-open",
+                                        new_meta,
+                                    ]).returncode
                                 elif system == "Darwin":
                                     res = subprocess.run(["open", new_meta]).returncode
                                 elif system == "Windows":
@@ -320,7 +321,7 @@ def __init__(
                         dedent(
                             """
                             Make sure a `latch_metadata` exists in the Snakemake
-                            project root or provide a metadata folder with the `--metadata-root` argument.""",
+                            project root or provide a metadata folder with the `--metadata-root` argument."""
                         ),
                         fg="red",
                     )
@@ -500,9 +501,7 @@ def get_old_centromere_info(self) -> Tuple[str, str]:
         response = tinyrequests.post(
             self.latch_provision_url,
             headers=headers,
-            json={
-                "public_key": self.public_key,
-            },
+            json={"public_key": self.public_key},
         )
 
         resp = response.json()
@@ -559,11 +558,7 @@ def nucleus_get_image(self, task_name: str, version: Optional[str] = None) -> st
 
         headers = {"Authorization": f"Bearer {self.token}"}
         response = tinyrequests.post(
-            self.latch_get_image_url,
-            headers=headers,
-            json={
-                "task_name": task_name,
-            },
+            self.latch_get_image_url, headers=headers, json={"task_name": task_name}
         )
 
         resp = response.json()