dayhoff-tools 1.0.3__tar.gz → 1.0.5__tar.gz

dayhoff_tools-1.0.5/PKG-INFO

@@ -0,0 +1,58 @@
+Metadata-Version: 2.3
+Name: dayhoff-tools
+Version: 1.0.5
+Summary: Common tools for all the repos at Dayhoff Labs
+Author: Daniel Martin-Alarcon
+Author-email: dma@dayhofflabs.com
+Requires-Python: >=3.10,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Provides-Extra: core
+Requires-Dist: biopython (>=1.84) ; extra == "core"
+Requires-Dist: boto3 (>=1.36.8) ; extra == "core"
+Requires-Dist: docker (>=7.1.0) ; extra == "core"
+Requires-Dist: fair-esm (>=2.0.0) ; extra == "core"
+Requires-Dist: firebase-admin (>=6.5.0)
+Requires-Dist: h5py (>=3.11.0) ; extra == "core"
+Requires-Dist: pyyaml (>=6.0)
+Requires-Dist: questionary (>=2.0.1) ; extra == "core"
+Requires-Dist: requests (>=2.31.0)
+Requires-Dist: typer (>=0.9.0)
+Description-Content-Type: text/markdown
+
+# dayhoff-tools
+
+A set of small, sharp tools for everyone at Dayhoff. Hosted on PyPi, so you can Poetry or pip install like everything else.
+
+## Installation
+
+The base package includes minimal dependencies required for core CLI functionality (like job running):
+
+```bash
+pip install dayhoff-tools
+# or
+poetry add dayhoff-tools
+```
+
+### Optional Dependencies
+
+You can install extra sets of dependencies using brackets. Available groups are:
+
+* `core`: Includes common data science and bioinformatics tools (`biopython`, `boto3`, `docker`, `fair-esm`, `h5py`, `questionary`).
+* `dev`: Includes development and testing tools (`black`, `pytest`, `pandas`, `numpy`, `torch`, etc.).
+* `all`: Includes all dependencies from both `core` and `dev`.
+
+**Examples:**
+
+```bash
+# Install with core dependencies
+pip install 'dayhoff-tools[core]'
+poetry add 'dayhoff-tools[core]'
+
+# Install with all dependencies
+pip install 'dayhoff-tools[all]'
+poetry add 'dayhoff-tools[all]'
+```

{dayhoff_tools-1.0.3 → dayhoff_tools-1.0.5}/dayhoff_tools/cli/cloud_commands.py

@@ -585,7 +585,8 @@ def aws_interactive():
                 )
 
         elif choice == "Show status":
-            aws_status()
+            # Fix: Explicitly pass None for the profile parameter
+            aws_status(profile=None)
 
         elif choice == "Exit":
             print(f"To activate profile {current_profile} in your current shell, run:")

{dayhoff_tools-1.0.3 → dayhoff_tools-1.0.5}/dayhoff_tools/cli/main.py

@@ -10,6 +10,7 @@ from dayhoff_tools.cli.utility_commands import (
     import_from_warehouse_typer,
     rebuild_devcontainer_file,
     test_github_actions_locally,
+    update_dayhoff_tools,
 )
 
 app = typer.Typer()
@@ -18,6 +19,7 @@ app = typer.Typer()
 app.command("clean")(delete_local_branch)
 app.command("gha")(test_github_actions_locally)
 app.command("rebuild")(rebuild_devcontainer_file)
+app.command("update")(update_dayhoff_tools)
 app.command("wadd")(add_to_warehouse_typer)
 app.command("wancestry")(get_ancestry)
 app.command("wimport")(import_from_warehouse_typer)

{dayhoff_tools-1.0.3 → dayhoff_tools-1.0.5}/dayhoff_tools/cli/utility_commands.py

@@ -251,3 +251,17 @@ def build_and_upload_wheel(bump_part: str = "patch"):
         print(f"Error during build/upload: {e}")
     except Exception as e:
         print(f"An unexpected error occurred: {e}")
+
+
+def update_dayhoff_tools():
+    """Update the dayhoff-tools package to the latest version using poetry."""
+    try:
+        print("Updating dayhoff-tools to the latest version...")
+        subprocess.run(["poetry", "update", "dayhoff-tools"], check=True)
+        print("Update complete!")
+    except subprocess.CalledProcessError as e:
+        print(f"Error occurred while updating: {e}")
+        sys.exit(1)
+    except FileNotFoundError:
+        print("Error: 'poetry' command not found. Make sure Poetry is installed.")
+        sys.exit(1)

dayhoff_tools-1.0.5/pyproject.toml

@@ -0,0 +1,53 @@
+[build-system]
+requires = ["poetry-core>=2.0"]
+build-backend = "poetry.core.masonry.api"
+
+[project]
+name = "dayhoff-tools"
+version = "1.0.5"
+description = "Common tools for all the repos at Dayhoff Labs"
+authors = [
+    {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
+]
+readme = "README.md"
+# Just enough deps to use the job_runner
+dependencies = [
+    "firebase-admin>=6.5.0",
+    "pyyaml>=6.0",
+    "requests>=2.31.0",
+    "typer>=0.9.0",
+]
+
+[project.optional-dependencies]
+# Deps we expect to need to bring to new repos
+core = [
+    "biopython>=1.84",
+    "boto3>=1.36.8",
+    "docker>=7.1.0",
+    "fair-esm>=2.0.0",
+    "h5py>=3.11.0",
+    "questionary>=2.0.1",
+]
+
+[tool.poetry.group.dev.dependencies]
+black = "^25.1.0"
+colorlog = "^6.8.2"
+dvc = "^3.48.2"
+dvc-gs = "^3.0.1"
+flake8 = "^7.0.0"
+isort = "^5.13.2"
+pylance = "^0.10.2"
+pylint = "^3.1.0"
+pytest = "^8.0.2"
+pytest-cov = "^4.1.0"
+pytest-mock = "^3.12.0"
+ipykernel = "^6.29.5"
+
+[project.scripts]
+dh = "dayhoff_tools.cli.main:app"
+
+[tool.poetry]
+package-mode = true
+
+[tool.poetry.dependencies]
+python = ">=3.10,<4.0"

dayhoff_tools-1.0.3/PKG-INFO

@@ -1,99 +0,0 @@
-Metadata-Version: 2.3
-Name: dayhoff-tools
-Version: 1.0.3
-Summary: Common tools for all the repos at Dayhoff Labs
-Author: Daniel Martin-Alarcon
-Author-email: dma@dayhofflabs.com
-Requires-Python: >=3.10,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Provides-Extra: all
-Provides-Extra: core
-Provides-Extra: dev
-Requires-Dist: biopython (>=1.84) ; extra == "all"
-Requires-Dist: biopython (>=1.84) ; extra == "core"
-Requires-Dist: black (>=25.1.0) ; extra == "all"
-Requires-Dist: black (>=25.1.0) ; extra == "dev"
-Requires-Dist: boto3 (>=1.36.8) ; extra == "all"
-Requires-Dist: boto3 (>=1.36.8) ; extra == "core"
-Requires-Dist: colorlog (>=6.8.2) ; extra == "all"
-Requires-Dist: colorlog (>=6.8.2) ; extra == "dev"
-Requires-Dist: docker (>=7.1.0) ; extra == "all"
-Requires-Dist: docker (>=7.1.0) ; extra == "core"
-Requires-Dist: dvc (>=3.48.2) ; extra == "all"
-Requires-Dist: dvc (>=3.48.2) ; extra == "dev"
-Requires-Dist: dvc-gs (>=3.0.1) ; extra == "all"
-Requires-Dist: dvc-gs (>=3.0.1) ; extra == "dev"
-Requires-Dist: fair-esm (>=2.0.0) ; extra == "all"
-Requires-Dist: fair-esm (>=2.0.0) ; extra == "core"
-Requires-Dist: firebase-admin (>=6.5.0)
-Requires-Dist: flake8 (>=7.0.0) ; extra == "all"
-Requires-Dist: flake8 (>=7.0.0) ; extra == "dev"
-Requires-Dist: h5py (>=3.11.0) ; extra == "all"
-Requires-Dist: h5py (>=3.11.0) ; extra == "core"
-Requires-Dist: isort (>=5.13.2) ; extra == "all"
-Requires-Dist: isort (>=5.13.2) ; extra == "dev"
-Requires-Dist: numpy (<2.0.0) ; extra == "all"
-Requires-Dist: numpy (<2.0.0) ; extra == "dev"
-Requires-Dist: pandas (>=2.2.3) ; extra == "dev"
-Requires-Dist: pylance (>=0.10.2) ; extra == "all"
-Requires-Dist: pylance (>=0.10.2) ; extra == "dev"
-Requires-Dist: pylint (>=3.1.0) ; extra == "all"
-Requires-Dist: pylint (>=3.1.0) ; extra == "dev"
-Requires-Dist: pytest (>=8.0.2) ; extra == "all"
-Requires-Dist: pytest (>=8.0.2) ; extra == "dev"
-Requires-Dist: pytest-cov (>=4.1.0) ; extra == "all"
-Requires-Dist: pytest-cov (>=4.1.0) ; extra == "dev"
-Requires-Dist: pytest-mock (>=3.12.0) ; extra == "all"
-Requires-Dist: pytest-mock (>=3.12.0) ; extra == "dev"
-Requires-Dist: pyyaml (>=6.0)
-Requires-Dist: questionary (>=2.0.1) ; extra == "all"
-Requires-Dist: questionary (>=2.0.1) ; extra == "core"
-Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "all"
-Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "dev"
-Requires-Dist: requests (>=2.31.0)
-Requires-Dist: torch (>=1.10.0) ; extra == "all"
-Requires-Dist: torch (>=1.10.0) ; extra == "dev"
-Requires-Dist: torchvision (>=0.11.0) ; extra == "all"
-Requires-Dist: torchvision (>=0.11.0) ; extra == "dev"
-Requires-Dist: transformers (>=4.20.0) ; extra == "all"
-Requires-Dist: transformers (>=4.36.2) ; extra == "dev"
-Requires-Dist: typer (>=0.9.0)
-Description-Content-Type: text/markdown
-
-# dayhoff-tools
-
-A set of small, sharp tools for everyone at Dayhoff. Hosted on PyPi, so you can Poetry or pip install like everything else.
-
-## Installation
-
-The base package includes minimal dependencies required for core CLI functionality (like job running):
-
-```bash
-pip install dayhoff-tools
-# or
-poetry add dayhoff-tools
-```
-
-### Optional Dependencies
-
-You can install extra sets of dependencies using brackets. Available groups are:
-
-* `core`: Includes common data science and bioinformatics tools (`biopython`, `boto3`, `docker`, `fair-esm`, `h5py`, `questionary`).
-* `dev`: Includes development and testing tools (`black`, `pytest`, `pandas`, `numpy`, `torch`, etc.).
-* `all`: Includes all dependencies from both `core` and `dev`.
-
-**Examples:**
-
-```bash
-# Install with core dependencies
-pip install 'dayhoff-tools[core]'
-poetry add 'dayhoff-tools[core]'
-
-# Install with all dependencies
-pip install 'dayhoff-tools[all]'
-poetry add 'dayhoff-tools[all]'
-```

dayhoff_tools-1.0.3/pyproject.toml

@@ -1,86 +0,0 @@
-[build-system]
-requires = ["poetry-core>=2.0"]
-build-backend = "poetry.core.masonry.api"
-
-[project]
-name = "dayhoff-tools"
-version = "1.0.3"
-description = "Common tools for all the repos at Dayhoff Labs"
-authors = [
-    {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
-]
-readme = "README.md"
-requires-python = ">=3.10,<4.0"
-# Just enough deps to use the job_runner
-dependencies = [
-    "firebase-admin>=6.5.0",
-    "pyyaml>=6.0",
-    "requests>=2.31.0",
-    "typer>=0.9.0",
-]
-
-[project.optional-dependencies]
-# Deps we expect to need to bring to new repos
-core = [
-    "biopython>=1.84",
-    "boto3>=1.36.8",
-    "docker>=7.1.0",
-    "fair-esm>=2.0.0",
-    "h5py>=3.11.0",
-    "questionary>=2.0.1",
-]
-
-# deps we expect to find in other repos, and don't want to interfere with
-dev = [
-    "black>=25.1.0",
-    "colorlog>=6.8.2",
-    "dvc>=3.48.2",
-    "dvc-gs>=3.0.1",
-    "flake8>=7.0.0",
-    "isort>=5.13.2",
-    "numpy<2.0.0",
-    "pandas>=2.2.3",
-    "pylance>=0.10.2", 
-    "pylint>=3.1.0",
-    "pytest>=8.0.2",
-    "pytest-cov>=4.1.0",
-    "pytest-mock>=3.12.0",
-    "rdkit-pypi>=2022.9.5",
-    "torch>=1.10.0",
-    "torchvision>=0.11.0",
-    "transformers>=4.36.2",
-]
-
-all = [
-    # Core dependencies
-    "biopython>=1.84",
-    "boto3>=1.36.8",
-    "docker>=7.1.0",
-    "fair-esm>=2.0.0",
-    "h5py>=3.11.0",
-    "questionary>=2.0.1",
-    
-    # Dev dependencies
-    "black>=25.1.0",
-    "colorlog>=6.8.2",
-    "dvc>=3.48.2",
-    "dvc-gs>=3.0.1",
-    "flake8>=7.0.0",
-    "isort>=5.13.2",
-    "numpy<2.0.0",
-    "pylance>=0.10.2", 
-    "pylint>=3.1.0",
-    "pytest>=8.0.2",
-    "pytest-cov>=4.1.0",
-    "pytest-mock>=3.12.0",
-    "rdkit-pypi>=2022.9.5",
-    "torch>=1.10.0",
-    "torchvision>=0.11.0",
-    "transformers>=4.20.0",
-]
-
-[project.scripts]
-dh = "dayhoff_tools.cli.main:app"
-
-[tool.poetry]
-package-mode = true