dayhoff-tools 1.1.10__py3-none-any.whl → 1.13.12__py3-none-any.whl

dayhoff_tools/warehouse.py

@@ -1,11 +1,91 @@
 import os
 import subprocess
+import sys
 from datetime import datetime
 from io import StringIO
 from pathlib import Path
 from zoneinfo import ZoneInfo
 
-from ruamel.yaml import YAML
+# Import cloud helper lazily inside functions to avoid heavy deps at module load
+
+
+def _find_project_root() -> Path | None:
+    """
+    Find the project root by searching upwards from the current directory for
+    a `.git` directory or a `pyproject.toml` file.
+
+    Returns:
+        The path to the project root, or None if not found.
+    """
+    current_dir = Path.cwd().resolve()
+    while current_dir != current_dir.parent:
+        if (current_dir / ".git").is_dir() or (
+            current_dir / "pyproject.toml"
+        ).is_file():
+            return current_dir
+        current_dir = current_dir.parent
+    # Check the final directory in the hierarchy (e.g., '/')
+    if (current_dir / ".git").is_dir() or (current_dir / "pyproject.toml").is_file():
+        return current_dir
+    return None
+
+
+def _warn_if_gcp_default_sa(force_prompt: bool = False) -> None:
+    """Warn the user when the active gcloud principal is the default VM service
+    account.  See detailed docstring later in file (duplicate for early
+    availability)."""
+
+    from dayhoff_tools.cli import cloud_commands as _cc
+
+    try:
+        impersonation = _cc._get_current_gcp_impersonation()
+        user = _cc._get_current_gcp_user()
+        active = impersonation if impersonation != "None" else user
+        short = _cc._get_short_name(active)
+
+        # Determine if user creds are valid
+        auth_valid = _cc._is_gcp_user_authenticated()
+    except Exception:
+        # If any helper errors out, don't block execution
+        return
+
+    problem_type = None  # "default_sa" | "stale"
+    if short == "default VM service account":
+        problem_type = "default_sa"
+    elif not auth_valid:
+        problem_type = "stale"
+
+    if problem_type is None:
+        return  # Everything looks good
+
+    YELLOW = getattr(_cc, "YELLOW", "\033[0;33m")
+    BLUE = getattr(_cc, "BLUE", "\033[0;36m")
+    RED = getattr(_cc, "RED", "\033[0;31m")
+    NC = getattr(_cc, "NC", "\033[0m")
+
+    if problem_type == "default_sa":
+        msg_body = (
+            f"You are currently authenticated as the *default VM service account*.\n"
+            f"   This will block gsutil/DVC access to private buckets (e.g. warehouse)."
+        )
+    else:  # stale creds
+        msg_body = (
+            f"Your GCP credentials appear to be *expired/stale*.\n"
+            f"   Re-authenticate to refresh the access token."
+        )
+
+    print(
+        f"{YELLOW}⚠  {msg_body}{NC}\n"
+        f"{YELLOW}   Run {BLUE}dh gcp login{YELLOW} or {BLUE}dh gcp use-devcon{YELLOW} before retrying.{NC}",
+        file=sys.stderr,
+    )
+
+    if force_prompt and sys.stdin.isatty() and sys.stdout.isatty():
+        import questionary
+
+        if not questionary.confirm("Proceed anyway?", default=False).ask():
+            print(f"{RED}Aborted due to unsafe GCP credentials.{NC}", file=sys.stderr)
+            raise SystemExit(1)
 
 
 def human_readable_size(size_bytes):
@@ -74,6 +154,8 @@ def format_yaml_with_meta_spacing(yaml_str: str) -> str:
 
 def update_dvc_files(directory):
     """Traverse directory and update .dvc files with human-readable size, preserving existing formatting"""
+    from ruamel.yaml import YAML
+
     yaml = YAML()
     yaml.preserve_quotes = True
     yaml.indent(mapping=2, sequence=4, offset=2)
@@ -188,6 +270,8 @@ def import_from_warehouse(
         subprocess.run(command, check=True)
 
     # Copy meta section from warehouse_path to final_path.dvc
+    from ruamel.yaml import YAML
+
     yaml = YAML()
     yaml.preserve_quotes = True
     yaml.indent(mapping=2, sequence=4, offset=2)
@@ -248,6 +332,8 @@ def add_to_warehouse(
 
     # Process each ancestor .dvc file
     ancestors = []
+    from ruamel.yaml import YAML
+
     yaml_loader = YAML()
     yaml_loader.preserve_quotes = True
     yaml_loader.indent(mapping=2, sequence=4, offset=2)
@@ -416,3 +502,184 @@ def get_from_warehouse(
         subprocess.run(command, check=True)
 
     return final_path
+
+
+def get_ancestry(filepath: str) -> None:
+    """Take a .dvc file created from import, and generate an ancestry entry
+    that can be manually copied into other .dvc files."""
+    with open(filepath, "r") as file:
+        assert filepath.endswith(".dvc"), "ERROR: Not a .dvc file"
+        import yaml
+
+        ancestor_content = yaml.safe_load(file)
+
+        error_msg = "Unexpected file structure. Are you sure this is a .dvc file generated from `dvc import`?"
+        assert "deps" in ancestor_content, error_msg
+
+        error_msg = "Please only reference data imported from main branches."
+        assert "rev" not in ancestor_content["deps"][0]["repo"], error_msg
+
+        ancestor_info = {
+            "name": os.path.basename(ancestor_content["outs"][0]["path"]),
+            "file_md5_hash": ancestor_content["outs"][0]["md5"],
+            "size": ancestor_content["outs"][0]["size"],
+            "repo_url": ancestor_content["deps"][0]["repo"]["url"],
+            "repo_path": ancestor_content["deps"][0]["path"],
+            "commit_hash": ancestor_content["deps"][0]["repo"]["rev_lock"],
+        }
+        print()
+        yaml.safe_dump(
+            [ancestor_info], sys.stdout, default_flow_style=False, sort_keys=False
+        )
+
+
+def import_from_warehouse_typer() -> None:
+    """Import a file from warehouse.
+
+    Emits an early warning if the active GCP credentials are the *default VM
+    service account* because this will prevent DVC/gsutil from accessing the
+    warehouse bucket.  The user can abort the command when running
+    interactively.
+    """
+
+    # Early-exit guard for wrong GCP credentials
+    _warn_if_gcp_default_sa(force_prompt=True)
+
+    # Import only when the function is called
+    import questionary
+
+    # Ensure execution from root directory
+    project_root = _find_project_root()
+    cwd = Path.cwd()
+    if not project_root or project_root != cwd:
+        error_msg = (
+            "This command must be run from the project's root directory, which is"
+            " expected to contain a `.git` folder or a `pyproject.toml` file.\n"
+            f"Current directory: {cwd}"
+        )
+        if project_root:
+            error_msg += f"\nDetected project root: {project_root}"
+        raise Exception(error_msg)
+
+    # Use questionary for prompts instead of typer
+    warehouse_path = questionary.text("Warehouse path:").ask()
+
+    # Provide multiple-choice options for output folder
+    output_folder_choice = questionary.select(
+        "Output folder:",
+        choices=["data/imports", "same_as_warehouse", "Custom path..."],
+    ).ask()
+
+    # If custom path is selected, ask for the path
+    if output_folder_choice == "Custom path...":
+        output_folder = questionary.text("Enter custom output folder:").ask()
+    else:
+        output_folder = output_folder_choice
+
+    branch = questionary.text("Branch (default: main):", default="main").ask()
+
+    final_path = import_from_warehouse(
+        warehouse_path=warehouse_path,
+        output_folder=output_folder,
+        branch=branch,
+    )
+
+
+def get_from_warehouse_typer() -> None:
+    """Get a file from warehouse using `dvc get`.
+
+    Emits an early warning if the active GCP credentials are the *default VM
+    service account* because this will prevent DVC/gsutil from accessing the
+    warehouse bucket.  The user can abort the command when running
+    interactively.
+    """
+
+    # Early-exit guard for wrong GCP credentials
+    _warn_if_gcp_default_sa(force_prompt=True)
+
+    # Import only when the function is called
+    import questionary
+
+    # Ensure execution from root directory
+    project_root = _find_project_root()
+    cwd = Path.cwd()
+    if not project_root or project_root != cwd:
+        error_msg = (
+            "This command must be run from the project's root directory, which is"
+            " expected to contain a `.git` folder or a `pyproject.toml` file.\n"
+            f"Current directory: {cwd}"
+        )
+        if project_root:
+            error_msg += f"\nDetected project root: {project_root}"
+        raise Exception(error_msg)
+
+    # Use questionary for prompts instead of typer
+    warehouse_path = questionary.text("Warehouse path:").ask()
+
+    # Provide multiple-choice options for output folder
+    output_folder_choice = questionary.select(
+        "Output folder:",
+        choices=["data/imports", "same_as_warehouse", "Custom path..."],
+    ).ask()
+
+    # If custom path is selected, ask for the path
+    if output_folder_choice == "Custom path...":
+        output_folder = questionary.text("Enter custom output folder:").ask()
+    else:
+        output_folder = output_folder_choice
+
+    branch = questionary.text("Branch (default: main):", default="main").ask()
+
+    final_path = get_from_warehouse(
+        warehouse_path=warehouse_path,
+        output_folder=output_folder,
+        branch=branch,
+    )
+
+
+def add_to_warehouse_typer() -> None:
+    """Add a new data file to warehouse and enrich its generated .dvc file.
+
+    As with *dh wimport*, this command fails when the user is logged in with
+    the default VM service account.  A guard therefore warns the user first
+    and allows them to abort interactively.
+    """
+
+    # Early-exit guard for wrong GCP credentials
+    _warn_if_gcp_default_sa(force_prompt=True)
+
+    # Import only when the function is called
+    import questionary
+
+    # Ensure execution from root directory
+    project_root = _find_project_root()
+    cwd = Path.cwd()
+    if not project_root or project_root != cwd:
+        error_msg = (
+            "This command must be run from the project's root directory, which is"
+            " expected to contain a `.git` folder or a `pyproject.toml` file.\n"
+            f"Current directory: {cwd}"
+        )
+        if project_root:
+            error_msg += f"\nDetected project root: {project_root}"
+        raise Exception(error_msg)
+
+    # Prompt for the data file path
+    warehouse_path = questionary.text("Data file to be registered:").ask()
+
+    # Prompt for the ancestor .dvc file paths
+    ancestor_dvc_paths = []
+    print("\nEnter the path of all ancestor .dvc files (or hit Enter to finish).")
+    print("These files must be generated by `dvc import` or `dh wimport`.")
+    while True:
+        ancestor_path = questionary.text("Ancestor path: ").ask()
+        if ancestor_path:
+            ancestor_dvc_paths.append(ancestor_path)
+        else:
+            print()
+            break
+
+    dvc_path = add_to_warehouse(
+        warehouse_path=warehouse_path,
+        ancestor_dvc_paths=ancestor_dvc_paths,
+    )

{dayhoff_tools-1.1.10.dist-info → dayhoff_tools-1.13.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: dayhoff-tools
-Version: 1.1.10
+Version: 1.13.12
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com
@@ -10,23 +10,36 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Provides-Extra: embedders
 Provides-Extra: full
 Requires-Dist: biopython (>=1.84) ; extra == "full"
-Requires-Dist: boto3 (>=1.36.8) ; extra == "full"
+Requires-Dist: biopython (>=1.85) ; extra == "embedders"
+Requires-Dist: boto3 (>=1.36.8)
 Requires-Dist: docker (>=7.1.0) ; extra == "full"
+Requires-Dist: fair-esm (>=2.0.0) ; extra == "embedders"
 Requires-Dist: fair-esm (>=2.0.0) ; extra == "full"
 Requires-Dist: firebase-admin (>=6.5.0)
 Requires-Dist: h5py (>=3.11.0) ; extra == "full"
-Requires-Dist: pandas (>=2.2.3) ; extra == "full"
+Requires-Dist: h5py (>=3.13.0) ; extra == "embedders"
+Requires-Dist: numpy (>=1.26.4) ; extra == "embedders"
+Requires-Dist: pandas (>=2.2.0,<2.2.3) ; extra == "embedders"
+Requires-Dist: pandas (>=2.2.0,<2.2.3) ; extra == "full"
 Requires-Dist: pyyaml (>=6.0)
 Requires-Dist: questionary (>=2.0.1)
 Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
 Requires-Dist: requests (>=2.31.0)
+Requires-Dist: sentencepiece (>=0.2.0) ; extra == "embedders"
 Requires-Dist: sentencepiece (>=0.2.0) ; extra == "full"
 Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0) ; extra == "full"
 Requires-Dist: toml (>=0.10)
+Requires-Dist: torch (>=2.4.0) ; extra == "embedders"
+Requires-Dist: tqdm (>=4.67.1) ; extra == "embedders"
+Requires-Dist: tqdm (>=4.67.1) ; extra == "full"
 Requires-Dist: transformers (==4.36.2) ; extra == "full"
+Requires-Dist: transformers (>=4.36.2) ; extra == "embedders"
 Requires-Dist: typer (>=0.9.0)
+Requires-Dist: tzdata (>=2025.2)
 Description-Content-Type: text/markdown
 
 # dayhoff-tools
@@ -40,7 +53,9 @@ The base package includes minimal dependencies required for core CLI functionali
 ```bash
 pip install dayhoff-tools
 # or
-poetry add dayhoff-tools
+uv add dayhoff-tools
+# or, for the special case of installing it in the DHT repo itself,
+uv pip install -e .[full]
 ```
 
 ### Optional Dependencies

dayhoff_tools-1.13.12.dist-info/RECORD

@@ -0,0 +1,54 @@
+dayhoff_tools/__init__.py,sha256=M5zThPyEBRYa5CfwlzKhcqTevWn3OKu62cjV6Zqie2A,469
+dayhoff_tools/chemistry/standardizer.py,sha256=uMn7VwHnx02nc404eO6fRuS4rsl4dvSPf2ElfZDXEpY,11188
+dayhoff_tools/chemistry/utils.py,sha256=jt-7JgF-GeeVC421acX-bobKbLU_X94KNOW24p_P-_M,2257
+dayhoff_tools/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+dayhoff_tools/cli/cloud_commands.py,sha256=xrWQZm48e09GTh8RmYh3JqXUzW8mMy07dHk_77LqZx8,41199
+dayhoff_tools/cli/engine1/__init__.py,sha256=RE45X2IPCNUvQp6_OHI2lbjwoqexkH3roUPccIHkeJo,9540
+dayhoff_tools/cli/engine1/engine_core.py,sha256=TECO6766GCZTtbxOY7QRggwmjpMH9JZSuxjbwF46unU,27061
+dayhoff_tools/cli/engine1/engine_lifecycle.py,sha256=_Dk-EZs_qbm8APdOuGOuxhlbK6RgkkoLk2nrwKoo1-A,4519
+dayhoff_tools/cli/engine1/engine_maintenance.py,sha256=S9w2_Ko2C3zKpzOux-iG8QUYn0sIua6oJkC8d-7HVxw,16301
+dayhoff_tools/cli/engine1/engine_management.py,sha256=s_H3FtMlKsdfzR8pwV-j2W2QX-Fypkqj2kPC0aTqC1A,19072
+dayhoff_tools/cli/engine1/shared.py,sha256=Ecx6I1jtzmxQDn3BezKpgpQ4SJeZf4SZjUCLg-67p80,16844
+dayhoff_tools/cli/engine1/studio_commands.py,sha256=VwTQujz32-uMcYusDRE73SdzRpgvIkv7ZAF4zRv6AzA,30266
+dayhoff_tools/cli/engines_studios/__init__.py,sha256=E6aG0C6qjJnJuClemSKRFlYvLUL49MQZOvfqNQ7SDKs,159
+dayhoff_tools/cli/engines_studios/api_client.py,sha256=7puTEpr3ukcguZr5aqRaSXLKM9Et799lnXwiywPvPz8,13459
+dayhoff_tools/cli/engines_studios/auth.py,sha256=rwetV5hp4jSvK8FyvKgXCnezLOZx1aW8oiSDc6U83iE,5189
+dayhoff_tools/cli/engines_studios/engine-studio-cli.md,sha256=or4k7ZZKPMTkvu67PdcUTE2_cxjnj0HQxxTuJZR1uiA,29924
+dayhoff_tools/cli/engines_studios/engine_commands.py,sha256=8utssuiLfxrff3Pk3PjMSUIVMU83mm9N8-Ny1uQr9es,38371
+dayhoff_tools/cli/engines_studios/progress.py,sha256=VW70t7sEHlbLpCi6LOaY19Rp1Kx6Rt9CKNnmaZWFteA,9496
+dayhoff_tools/cli/engines_studios/simulators/cli-simulators.md,sha256=FZJl6nehdr2Duht2cx3yijcak0yKyOaHTrTzvFTAfZs,4976
+dayhoff_tools/cli/engines_studios/simulators/demo.sh,sha256=8tYABSCxLNXqGs-4r071V9mpKNZ5DTQ34WZ-v3d5s94,5364
+dayhoff_tools/cli/engines_studios/simulators/engine_list_simulator.py,sha256=vUrB6gV9UX74L5uCRMTVcPmk_1ZOuP1jYJf6cMP7dOE,9525
+dayhoff_tools/cli/engines_studios/simulators/engine_status_simulator.py,sha256=KUm3gA2MiRgGrQV7KURhb5zabM18-30z_ugRjiq5iso,13024
+dayhoff_tools/cli/engines_studios/simulators/idle_status_simulator.py,sha256=F_MfEXdPKNVDCKgJV72QyU2oMG8hLt-Bwic4yFadRXE,17570
+dayhoff_tools/cli/engines_studios/simulators/simulator_utils.py,sha256=HA08pIMJWV3OFrWj3Ca8GldvgJZfFoTOloyLK0UWMgA,6729
+dayhoff_tools/cli/engines_studios/simulators/studio_list_simulator.py,sha256=ntizeR0BJLdJOwCRBKPajc2xT-BL7SNnONxfgxXDgr8,11609
+dayhoff_tools/cli/engines_studios/simulators/studio_status_simulator.py,sha256=6WvpnRawJVaQf_H81zuR1_66igRRVxPxjAt8e69xjp4,5394
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+dayhoff_tools/cli/main.py,sha256=Nz_jtbppmvWKHZydQ0nkt_eejccJE90ces8xCGrerdY,7086
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+dayhoff_tools/deployment/base.py,sha256=uZnFvnPQx6pH_HmJbdThweAs3BrxMaDohpE3iX_-yk4,18377
+dayhoff_tools/deployment/deploy_aws.py,sha256=1j16aE4hmln4pQVtcSGuIGVWbOBfWwveytvihjofADo,21519
+dayhoff_tools/deployment/deploy_gcp.py,sha256=xgaOVsUDmP6wSEMYNkm1yRNcVskfdz80qJtCulkBIAM,8860
+dayhoff_tools/deployment/deploy_utils.py,sha256=KyUFZZWn8NGT9QpR0HGqkX-huOFubvYCabko9SlC5Gg,26516
+dayhoff_tools/deployment/job_runner.py,sha256=hljvFpH2Bw96uYyUup5Ths72PZRL_X27KxlYzBMgguo,5086
+dayhoff_tools/deployment/processors.py,sha256=LM0CQbr4XCb3AtLbrcuDQm4tYPXsoNqgVJ4WQYDjzJc,12406
+dayhoff_tools/deployment/swarm.py,sha256=YJfvVOcAS8cYcIj2fiN4qwC2leh0I9w5A4px8ZWSF6g,22833
+dayhoff_tools/embedders.py,sha256=1THnmio4FYkBswy_xkIiwT-ZOEMn6ZLbTAa-Uz0-kyE,36615
+dayhoff_tools/fasta.py,sha256=USdemH4c_dNhWXOTAhldvlDi8eLHogsy0YSrOnODB5I,50773
+dayhoff_tools/file_ops.py,sha256=JlGowvr-CUJFidV-4g_JmhUTN9bsYuaxtqKmnKomm-Q,8506
+dayhoff_tools/h5.py,sha256=j1nxxaiHsMidVX_XwB33P1Pz9d7K8ZKiDZwJWQUUQSY,21158
+dayhoff_tools/intake/gcp.py,sha256=uCeEskhbEwJIYpN6ne6siT1dbpTizCjjel-hRe0kReE,3030
+dayhoff_tools/intake/gtdb.py,sha256=58JNLWpr3LkXiIq-ubAcEFeR5DyN9YrA-YEoQI_FzlA,10608
+dayhoff_tools/intake/kegg.py,sha256=SaVbumB4leNTSevamT29yIqHurejw1wmcCC32D5Qyco,965
+dayhoff_tools/intake/mmseqs.py,sha256=uEYzRsthJAlUeRYNCfFtJFE73SbuhfUIS1ygYFkhmtw,6435
+dayhoff_tools/intake/structure.py,sha256=ufN3gAodQxhnt7psK1VTQeu9rKERmo_PhoxIbB4QKMw,27660
+dayhoff_tools/intake/uniprot.py,sha256=BZYJQF63OtPcBBnQ7_P9gulxzJtqyorgyuDiPeOJqE4,16456
+dayhoff_tools/logs.py,sha256=DKdeP0k0kliRcilwvX0mUB2eipO5BdWUeHwh-VnsICs,838
+dayhoff_tools/sqlite.py,sha256=jV55ikF8VpTfeQqqlHSbY8OgfyfHj8zgHNpZjBLos_E,18672
+dayhoff_tools/warehouse.py,sha256=UETBtZD3r7WgvURqfGbyHlT7cxoiVq8isjzMuerKw8I,24475
+dayhoff_tools-1.13.12.dist-info/METADATA,sha256=VtmgJEzSIBc552oggyiNJXoZJZ-0L4aNrPhfv-yKeGc,2981
+dayhoff_tools-1.13.12.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+dayhoff_tools-1.13.12.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.13.12.dist-info/RECORD,,

{dayhoff_tools-1.1.10.dist-info → dayhoff_tools-1.13.12.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.3
+Generator: poetry-core 2.2.1
 Root-Is-Purelib: true
 Tag: py3-none-any

dayhoff_tools-1.1.10.dist-info/RECORD

@@ -1,32 +0,0 @@
-dayhoff_tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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