haplohub-cli 2.5.0__tar.gz → 2.6.0__tar.gz

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: haplohub-cli
-Version: 2.5.0
+Version: 2.6.0
 Summary: HaploHub Command Line Interface
 Author-email: Mike Polcari <mike@haplotype-labs.com>, Ilya Khrustalev <ilya@haplotype-labs.com>
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 Requires-Dist: click>=8.1.8
-Requires-Dist: haplohub<3,>=2.2.0
+Requires-Dist: haplohub<3,>=2.16.0
 Requires-Dist: pendulum>=3.0.0
 Requires-Dist: requests>=2.32.0
 Requires-Dist: rich>=13.9.4

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '2.5.0'
-__version_tuple__ = version_tuple = (2, 5, 0)
+__version__ = version = '2.6.0'
+__version_tuple__ = version_tuple = (2, 6, 0)
 
-__commit_id__ = commit_id = 'gcd8a204d2'
+__commit_id__ = commit_id = 'gaebb47593'

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli/commands/algorithm/result/__init__.py

@@ -17,10 +17,24 @@ def result():
 
 
 @result.command()
-def list(algorithm_version_id: Optional[str] = None, cohort_id: Optional[str] = None):
+@click.option("--algorithm", "-a", type=str, required=False, help="Filter by algorithm name (e.g. pgsc_calc)")
+@click.option("--version", "-v", type=str, required=False, help="Filter by algorithm version")
+@click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=False, help="Filter by cohort")
+@click.option("--member", "-m", type=types.HAPLOHUB_ID, required=False, help="Filter by member")
+@click.option("--sample", "-s", type=types.HAPLOHUB_ID, required=False, help="Filter by sample")
+def list(
+    algorithm: Optional[str] = None,
+    version: Optional[str] = None,
+    cohort: Optional[str] = None,
+    member: Optional[str] = None,
+    sample: Optional[str] = None,
+):
     return client.algorithm_result.list_algorithm_results(
-        algorithm_version_id=algorithm_version_id,
-        cohort_id=cohort_id,
+        algorithm=algorithm,
+        version=version,
+        cohort_id=cohort,
+        member_id=member,
+        sample_id=sample,
     )
 
 

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli/commands/cohort/__init__.py

@@ -36,7 +36,7 @@ def delete(id):
 
 @cohort.command()
 def accession():
-    return client.metadata.list_accession()
+    return client.accession.list_accession()
 
 
 cohort.add_command(biomarker.biomarker)

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli/commands/cohort/member/__init__.py

@@ -1,8 +1,9 @@
 import click
-from haplohub import CreateMemberRequest, UpdateMemberRequest
+from haplohub import CreateMemberRequest, DeleteMode, UpdateMemberRequest
 
 from haplohub_cli.core import types
 from haplohub_cli.core.api.client import client
+from haplohub_cli.core.deletion import DELETE_MODE_CHOICES, DELETE_MODE_HELP, confirm_hard_delete
 
 from . import report
 
@@ -23,14 +24,14 @@ def list(cohort: str):
 
 @member.command()
 @click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
-@click.option("--patient-id", "-p", type=str, required=False)
+@click.option("--external-id", "-x", type=str, required=False)
 @click.option("--first-name", "-fn", type=str, required=False)
 @click.option("--last-name", "-ln", type=str, required=False)
 @click.option("--gender", "-g", type=str, required=False)
 @click.option("--birth-date", "-bd", type=str, required=False)
-def create(cohort, patient_id=None, first_name=None, last_name=None, gender=None, birth_date=None):
+def create(cohort, external_id=None, first_name=None, last_name=None, gender=None, birth_date=None):
     request = CreateMemberRequest(
-        patient_id=patient_id,
+        external_id=external_id,
         first_name=first_name,
         last_name=last_name,
         gender=gender,
@@ -42,21 +43,31 @@ def create(cohort, patient_id=None, first_name=None, last_name=None, gender=None
 @member.command()
 @click.argument("id")
 @click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
-def delete(id, cohort):
-    return client.member.delete_member(cohort, id)
+@click.option(
+    "--mode",
+    "-m",
+    type=click.Choice(DELETE_MODE_CHOICES),
+    default=DeleteMode.SOFT.value,
+    show_default=True,
+    help=DELETE_MODE_HELP,
+)
+@click.option("--yes", "-y", is_flag=True, help="Skip the confirmation prompt for --mode hard.")
+def delete(id, cohort, mode, yes):
+    confirm_hard_delete(mode, "member", id, yes)
+    return client.member.delete_member(cohort, id, mode=mode)
 
 
 @member.command()
 @click.argument("id")
 @click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
-@click.option("--patient-id", "-p", type=str, required=False)
+@click.option("--external-id", "-x", type=str, required=False)
 @click.option("--first-name", "-fn", type=str, required=False)
 @click.option("--last-name", "-ln", type=str, required=False)
 @click.option("--gender", "-g", type=str, required=False)
 @click.option("--birth-date", "-bd", type=str, required=False)
-def update(id, cohort, patient_id=None, first_name=None, last_name=None, gender=None, birth_date=None):
+def update(id, cohort, external_id=None, first_name=None, last_name=None, gender=None, birth_date=None):
     request = UpdateMemberRequest(
-        patient_id=patient_id,
+        external_id=external_id,
         first_name=first_name,
         last_name=last_name,
         gender=gender,

haplohub_cli-2.6.0/haplohub_cli/commands/cohort/sample.py

@@ -0,0 +1,84 @@
+import click
+from haplohub import CreateSampleRequest, DeleteMode, UpdateSampleRequest
+
+from haplohub_cli.core import types
+from haplohub_cli.core.api.client import client
+from haplohub_cli.core.deletion import DELETE_MODE_CHOICES, DELETE_MODE_HELP, confirm_hard_delete
+
+
+@click.group()
+def sample():
+    """
+    Manage samples
+    """
+    pass
+
+
+@sample.command()
+@click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
+def list(cohort: str):
+    return client.sample.list_samples(cohort)
+
+
+@sample.command()
+@click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
+@click.option(
+    "--external-id",
+    "-x",
+    type=click.STRING,
+    required=False,
+    help="Sample identity, uppercase alphanumeric starting with a letter. Generated when omitted.",
+)
+@click.option("--member", "-m", type=types.HAPLOHUB_ID, required=False, help="Member to attach the sample to.")
+@click.option(
+    "--member-external-id",
+    "-xm",
+    type=click.STRING,
+    required=False,
+    help="Member to attach the sample to, by external id. The member is created when it does not exist.",
+)
+def create(cohort, external_id=None, member=None, member_external_id=None):
+    request = CreateSampleRequest(
+        external_id=external_id,
+        member_id=member,
+        member_external_id=member_external_id,
+    )
+    return client.sample.create_sample(cohort, request)
+
+
+@sample.command()
+@click.argument("id")
+@click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
+@click.option(
+    "--mode",
+    "-m",
+    type=click.Choice(DELETE_MODE_CHOICES),
+    default=DeleteMode.SOFT.value,
+    show_default=True,
+    help=DELETE_MODE_HELP,
+)
+@click.option("--yes", "-y", is_flag=True, help="Skip the confirmation prompt for --mode hard.")
+def delete(id, cohort, mode, yes):
+    confirm_hard_delete(mode, "sample", id, yes)
+    return client.sample.delete_sample(cohort, id, mode=mode)
+
+
+@sample.command()
+@click.argument("id")
+@click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
+@click.option("--member", "-m", type=types.HAPLOHUB_ID, required=False, help="Member to attach the sample to.")
+@click.option(
+    "--member-external-id",
+    "-xm",
+    type=click.STRING,
+    required=False,
+    help="Member to attach the sample to, by external id.",
+)
+def update(id, cohort, member=None, member_external_id=None):
+    # external_id is the sample's immutable identity, embedded in the BCFs; only the
+    # member association can be changed.
+    request = UpdateSampleRequest(
+        member_id=member,
+        member_external_id=member_external_id,
+    )
+    return client.sample.update_sample(cohort, id, request)

haplohub_cli-2.6.0/haplohub_cli/commands/cohort/tests/test_delete.py

@@ -0,0 +1,88 @@
+from unittest import TestCase
+from unittest.mock import patch
+
+from click.testing import CliRunner
+
+from haplohub_cli.commands.cohort.member import member
+from haplohub_cli.commands.cohort.sample import sample
+
+COHORT = "coh-abc123"
+MEMBER = "mbr-abc123"
+SAMPLE = "smp-abc123"
+
+
+class DeleteMemberTestCase(TestCase):
+    def setUp(self):
+        self.runner = CliRunner()
+
+    def run_delete(self, *args, input=None):
+        with patch("haplohub_cli.commands.cohort.member.client") as client:
+            result = self.runner.invoke(member, ["delete", MEMBER, "-c", COHORT, *args], input=input)
+        return result, client.member.delete_member
+
+    def test_defaults_to_soft(self):
+        result, delete_member = self.run_delete()
+
+        self.assertEqual(result.exit_code, 0, result.output)
+        delete_member.assert_called_once_with(COHORT, MEMBER, mode="soft")
+
+    def test_cascade_needs_no_confirmation(self):
+        result, delete_member = self.run_delete("--mode", "cascade")
+
+        self.assertEqual(result.exit_code, 0, result.output)
+        delete_member.assert_called_once_with(COHORT, MEMBER, mode="cascade")
+
+    def test_hard_asks_for_confirmation(self):
+        result, delete_member = self.run_delete("--mode", "hard", input="y\n")
+
+        self.assertEqual(result.exit_code, 0, result.output)
+        self.assertIn("cannot be undone", result.output)
+        delete_member.assert_called_once_with(COHORT, MEMBER, mode="hard")
+
+    def test_hard_aborts_when_declined(self):
+        result, delete_member = self.run_delete("--mode", "hard", input="n\n")
+
+        self.assertEqual(result.exit_code, 1)
+        delete_member.assert_not_called()
+
+    def test_hard_skips_confirmation_with_yes(self):
+        result, delete_member = self.run_delete("--mode", "hard", "--yes")
+
+        self.assertEqual(result.exit_code, 0, result.output)
+        self.assertNotIn("cannot be undone", result.output)
+        delete_member.assert_called_once_with(COHORT, MEMBER, mode="hard")
+
+    def test_rejects_an_unknown_mode(self):
+        result, delete_member = self.run_delete("--mode", "nuke")
+
+        self.assertEqual(result.exit_code, 2)
+        delete_member.assert_not_called()
+
+
+class DeleteSampleTestCase(TestCase):
+    def setUp(self):
+        self.runner = CliRunner()
+
+    def run_delete(self, *args, input=None):
+        with patch("haplohub_cli.commands.cohort.sample.client") as client:
+            result = self.runner.invoke(sample, ["delete", SAMPLE, "-c", COHORT, *args], input=input)
+        return result, client.sample.delete_sample
+
+    def test_defaults_to_soft(self):
+        result, delete_sample = self.run_delete()
+
+        self.assertEqual(result.exit_code, 0, result.output)
+        delete_sample.assert_called_once_with(COHORT, SAMPLE, mode="soft")
+
+    def test_hard_asks_for_confirmation(self):
+        result, delete_sample = self.run_delete("--mode", "hard", input="y\n")
+
+        self.assertEqual(result.exit_code, 0, result.output)
+        self.assertIn("cannot be undone", result.output)
+        delete_sample.assert_called_once_with(COHORT, SAMPLE, mode="hard")
+
+    def test_hard_aborts_when_declined(self):
+        result, delete_sample = self.run_delete("--mode", "hard", input="n\n")
+
+        self.assertEqual(result.exit_code, 1)
+        delete_sample.assert_not_called()

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli/commands/file.py

@@ -63,6 +63,21 @@ def download(cohort: str, file_id: str = None, file_path: str = None, output: st
     click.echo(f"File saved to {output}")
 
 
+def _resolve_file_id(cohort: str, file_path: str) -> str:
+    """Look a file up by its location.
+
+    The API deletes by id only - unlike downloads, which have a by-path endpoint - so
+    the path is resolved here to keep --file-path working on both commands.
+    """
+    listing = client.file.list_files(cohort, recursive=True)
+    wanted = file_path.lstrip("/")
+    for entry in listing.result.files:
+        if entry.location == wanted:
+            return entry.id
+
+    raise click.ClickException(f"No file at '{file_path}' in cohort {cohort}.")
+
+
 @file.command()
 @click.option("--cohort", "-c", type=click.STRING, required=True)
 @click.option("--file-id", "-i", type=click.STRING, required=False)
@@ -74,10 +89,10 @@ def delete(cohort: str, file_id: str = None, file_path: str = None):
     if not file_id and not file_path:
         raise click.UsageError("Must specify either --file-id or --file-path")
 
-    if file_id:
-        return client.file.delete_file(cohort, file_id)
+    if not file_id:
+        file_id = _resolve_file_id(cohort, file_path)
 
-    return client.file.delete_file_by_path(cohort, file_path)
+    return client.file.delete_file(cohort, file_id)
 
 
 @file.command()

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli/commands/metadata/__init__.py

@@ -13,4 +13,4 @@ def metadata():
 
 @metadata.command()
 def accession():
-    return client.metadata.list_accession()
+    return client.accession.list_accession()

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli/core/api/client.py

@@ -2,6 +2,7 @@ from functools import cached_property
 
 import click
 from haplohub import (
+    AccessionApi,
     AlgorithmApi,
     AlgorithmResultApi,
     ApiClient,
@@ -83,5 +84,9 @@ class Client:
     def algorithm_result(self):
         return AlgorithmResultApi(self.client)
 
+    @cached_property
+    def accession(self):
+        return AccessionApi(self.client)
+
 
 client = Client()

haplohub_cli-2.6.0/haplohub_cli/core/deletion.py

@@ -0,0 +1,28 @@
+import click
+from haplohub import DeleteMode
+
+# The generated client drops `mode` straight into the query string, so the commands pass
+# the plain value rather than the enum member.
+DELETE_MODE_CHOICES = [mode.value for mode in DeleteMode]
+
+DELETE_MODE_HELP = (
+    "How far the delete reaches. "
+    "soft: the record only. "
+    "cascade: the record plus everything derived from it, files included; recoverable. "
+    "hard: irreversible, erases the records permanently and removes every version of their files."
+)
+
+
+def confirm_hard_delete(mode: str, entity: str, identifier: str, assume_yes: bool) -> None:
+    """Guard `--mode hard`, which cannot be undone.
+
+    Softer modes leave the rows recoverable and the blobs restorable, so they go through
+    without a prompt.
+    """
+    if mode != DeleteMode.HARD.value or assume_yes:
+        return
+
+    click.confirm(
+        f"Permanently erase {entity} {identifier} and every version of its files? This cannot be undone.",
+        abort=True,
+    )

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli/formatters/generic.py

@@ -1,6 +1,7 @@
 from haplohub import (
     ErrorResponse,
-    ResultResponse,
+    GenericResponse,
+    SuccessResponse,
 )
 from rich.text import Text
 
@@ -12,8 +13,13 @@ def format_error_response(data: ErrorResponse):
     return Text(f"Error [{data.error.code}]: {data.error.message}", style="red")
 
 
-@register(ResultResponse)
-def format_result_response(data: ResultResponse):
+# The bare ResultResponse this used to render is gone from the SDK: the API returns
+# generic ResultResponse[T] wrappers, which generate as concrete per-payload classes.
+# SuccessResponse is what the operations carrying no payload of their own return,
+# deletes among them.
+@register(SuccessResponse)
+@register(GenericResponse)
+def format_success_response(data):
     if data.status == "success":
         return Text("Result: Operation successful", style="green")
     else:

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli/formatters/member.py

@@ -13,7 +13,7 @@ from haplohub_cli.formatters.decorators import register
 def format_member(data: MemberSchema):
     table = Table(title="Member", caption=f"Id: {utils.format_id(data.id)}")
     table.add_column("Id")
-    table.add_column("Patient ID")
+    table.add_column("External ID")
     table.add_column("First Name")
     table.add_column("Last Name")
     table.add_column("Gender")
@@ -21,7 +21,7 @@ def format_member(data: MemberSchema):
     table.add_column("Created")
     table.add_row(
         utils.format_id(data.id),
-        data.patient_id,
+        data.external_id,
         data.first_name,
         data.last_name,
         data.gender,
@@ -35,7 +35,7 @@ def format_member(data: MemberSchema):
 def format_members(data: PaginatedResponseMemberSchema):
     table = Table(title="Members", caption=f"Total: {data.total_count}")
     table.add_column("Id")
-    table.add_column("Patient ID")
+    table.add_column("External ID")
     table.add_column("First Name")
     table.add_column("Last Name")
     table.add_column("Gender")
@@ -45,7 +45,7 @@ def format_members(data: PaginatedResponseMemberSchema):
     for item in data.items:
         table.add_row(
             utils.format_id(item.id),
-            item.patient_id,
+            item.external_id,
             item.first_name,
             item.last_name,
             item.gender,

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli.egg-info/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: haplohub-cli
-Version: 2.5.0
+Version: 2.6.0
 Summary: HaploHub Command Line Interface
 Author-email: Mike Polcari <mike@haplotype-labs.com>, Ilya Khrustalev <ilya@haplotype-labs.com>
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 Requires-Dist: click>=8.1.8
-Requires-Dist: haplohub<3,>=2.2.0
+Requires-Dist: haplohub<3,>=2.16.0
 Requires-Dist: pendulum>=3.0.0
 Requires-Dist: requests>=2.32.0
 Requires-Dist: rich>=13.9.4

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli.egg-info/SOURCES.txt

@@ -39,12 +39,15 @@ haplohub_cli/commands/cohort/biomarker.py
 haplohub_cli/commands/cohort/sample.py
 haplohub_cli/commands/cohort/member/__init__.py
 haplohub_cli/commands/cohort/member/report.py
+haplohub_cli/commands/cohort/tests/__init__.py
+haplohub_cli/commands/cohort/tests/test_delete.py
 haplohub_cli/commands/metadata/__init__.py
 haplohub_cli/config/__init__.py
 haplohub_cli/config/config.py
 haplohub_cli/config/config_manager.py
 haplohub_cli/core/__init__.py
 haplohub_cli/core/checksum.py
+haplohub_cli/core/deletion.py
 haplohub_cli/core/network.py
 haplohub_cli/core/slug.py
 haplohub_cli/core/types.py

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli.egg-info/requires.txt

@@ -1,5 +1,5 @@
 click>=8.1.8
-haplohub<3,>=2.2.0
+haplohub<3,>=2.16.0
 pendulum>=3.0.0
 requests>=2.32.0
 rich>=13.9.4

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/haplohub_cli.egg-info/scm_file_list.json

@@ -1,69 +1,72 @@
 {
   "files": [
     ".pre-commit-config.yaml",
+    "pyproject.toml",
     "README.md",
     "uv.lock",
-    "pyproject.toml",
     ".gitignore",
-    "haplohub_cli/__init__.py",
+    ".github/dependabot.yml",
+    ".github/workflows/on_push_main.yml",
+    ".github/workflows/on_pr.yml",
     "haplohub_cli/settings.py",
+    "haplohub_cli/__init__.py",
     "haplohub_cli/cli.py",
+    "haplohub_cli/types/variant_range.py",
+    "haplohub_cli/types/__init__.py",
+    "haplohub_cli/formatters/cohort.py",
+    "haplohub_cli/formatters/generic.py",
+    "haplohub_cli/formatters/config.py",
+    "haplohub_cli/formatters/member.py",
+    "haplohub_cli/formatters/algorithm.py",
+    "haplohub_cli/formatters/formatter_registry.py",
+    "haplohub_cli/formatters/__init__.py",
+    "haplohub_cli/formatters/variant.py",
+    "haplohub_cli/formatters/algorithm_result.py",
+    "haplohub_cli/formatters/biomarker.py",
+    "haplohub_cli/formatters/metadata.py",
+    "haplohub_cli/formatters/sample.py",
+    "haplohub_cli/formatters/decorators.py",
+    "haplohub_cli/formatters/file.py",
+    "haplohub_cli/formatters/utils.py",
+    "haplohub_cli/commands/login.py",
+    "haplohub_cli/commands/config.py",
     "haplohub_cli/commands/__init__.py",
+    "haplohub_cli/commands/variant.py",
     "haplohub_cli/commands/version.py",
-    "haplohub_cli/commands/config.py",
     "haplohub_cli/commands/file.py",
-    "haplohub_cli/commands/variant.py",
-    "haplohub_cli/commands/login.py",
-    "haplohub_cli/commands/cohort/biomarker.py",
-    "haplohub_cli/commands/cohort/__init__.py",
-    "haplohub_cli/commands/cohort/sample.py",
-    "haplohub_cli/commands/cohort/member/__init__.py",
-    "haplohub_cli/commands/cohort/member/report.py",
     "haplohub_cli/commands/metadata/__init__.py",
     "haplohub_cli/commands/algorithm/__init__.py",
     "haplohub_cli/commands/algorithm/result/__init__.py",
-    "haplohub_cli/core/network.py",
-    "haplohub_cli/core/__init__.py",
-    "haplohub_cli/core/checksum.py",
-    "haplohub_cli/core/slug.py",
-    "haplohub_cli/core/upload.py",
-    "haplohub_cli/core/types.py",
-    "haplohub_cli/core/api/__init__.py",
-    "haplohub_cli/core/api/client.py",
-    "haplohub_cli/core/tests/test_checksum.py",
-    "haplohub_cli/core/tests/__init__.py",
-    "haplohub_cli/core/tests/test_slug.py",
-    "haplohub_cli/core/tests/test_network.py",
-    "haplohub_cli/auth/__init__.py",
+    "haplohub_cli/commands/cohort/__init__.py",
+    "haplohub_cli/commands/cohort/biomarker.py",
+    "haplohub_cli/commands/cohort/sample.py",
+    "haplohub_cli/commands/cohort/tests/test_delete.py",
+    "haplohub_cli/commands/cohort/tests/__init__.py",
+    "haplohub_cli/commands/cohort/member/report.py",
+    "haplohub_cli/commands/cohort/member/__init__.py",
+    "haplohub_cli/auth/auth_web_server.py",
     "haplohub_cli/auth/token_storage.py",
     "haplohub_cli/auth/auth.py",
+    "haplohub_cli/auth/__init__.py",
     "haplohub_cli/auth/oauth_client.py",
-    "haplohub_cli/auth/auth_web_server.py",
-    "haplohub_cli/auth/tests/test_token_storage.py",
-    "haplohub_cli/auth/tests/__init__.py",
     "haplohub_cli/auth/tests/test_auth_web_server.py",
+    "haplohub_cli/auth/tests/__init__.py",
+    "haplohub_cli/auth/tests/test_token_storage.py",
+    "haplohub_cli/config/config.py",
     "haplohub_cli/config/__init__.py",
     "haplohub_cli/config/config_manager.py",
-    "haplohub_cli/config/config.py",
-    "haplohub_cli/formatters/biomarker.py",
-    "haplohub_cli/formatters/__init__.py",
-    "haplohub_cli/formatters/algorithm.py",
-    "haplohub_cli/formatters/config.py",
-    "haplohub_cli/formatters/file.py",
-    "haplohub_cli/formatters/utils.py",
-    "haplohub_cli/formatters/member.py",
-    "haplohub_cli/formatters/cohort.py",
-    "haplohub_cli/formatters/decorators.py",
-    "haplohub_cli/formatters/formatter_registry.py",
-    "haplohub_cli/formatters/metadata.py",
-    "haplohub_cli/formatters/variant.py",
-    "haplohub_cli/formatters/algorithm_result.py",
-    "haplohub_cli/formatters/sample.py",
-    "haplohub_cli/formatters/generic.py",
-    "haplohub_cli/types/__init__.py",
-    "haplohub_cli/types/variant_range.py",
-    ".github/dependabot.yml",
-    ".github/workflows/on_pr.yml",
-    ".github/workflows/on_push_main.yml"
+    "haplohub_cli/core/types.py",
+    "haplohub_cli/core/network.py",
+    "haplohub_cli/core/deletion.py",
+    "haplohub_cli/core/checksum.py",
+    "haplohub_cli/core/__init__.py",
+    "haplohub_cli/core/slug.py",
+    "haplohub_cli/core/upload.py",
+    "haplohub_cli/core/tests/__init__.py",
+    "haplohub_cli/core/tests/test_checksum.py",
+    "haplohub_cli/core/tests/test_network.py",
+    "haplohub_cli/core/tests/test_slug.py",
+    "haplohub_cli/core/api/__init__.py",
+    "haplohub_cli/core/api/client.py"
   ]
 }

haplohub_cli-2.6.0/haplohub_cli.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "2.6.0",
+  "distance": 0,
+  "node": "gaebb47593fb0fda18b4541e27a7acec06b67aeab",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-08-04"
+}

{haplohub_cli-2.5.0 → haplohub_cli-2.6.0}/pyproject.toml

@@ -10,7 +10,7 @@ requires-python = ">=3.8"
 dynamic = ["version"]
 dependencies = [
     "click>=8.1.8",
-    "haplohub>=2.2.0,<3",
+    "haplohub>=2.16.0,<3",
     "pendulum>=3.0.0",
     "requests>=2.32.0",
     "rich>=13.9.4",

haplohub_cli-2.5.0/haplohub_cli/commands/cohort/sample.py

@@ -1,51 +0,0 @@
-import click
-from haplohub import CreateSampleRequest, UpdateSampleRequest
-
-from haplohub_cli.core import types
-from haplohub_cli.core.api.client import client
-
-
-@click.group()
-def sample():
-    """
-    Manage samples
-    """
-    pass
-
-
-@sample.command()
-@click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
-def list(cohort: str):
-    return client.sample.list_samples(cohort)
-
-
-@sample.command()
-@click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
-@click.option("--patient-id", "-p", type=click.STRING, required=False)
-@click.option("--sample-id", "-s", type=click.STRING, required=False)
-def create(cohort, sample_id=None, patient_id=None):
-    request = CreateSampleRequest(
-        sample_id=sample_id,
-        patient_id=patient_id,
-    )
-    return client.sample.create_sample(cohort, request)
-
-
-@sample.command()
-@click.argument("id")
-@click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
-def delete(id, cohort):
-    return client.sample.delete_sample(cohort, id)
-
-
-@sample.command()
-@click.argument("id")
-@click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True)
-@click.option("--patient-id", "-p", type=click.STRING, required=False)
-@click.option("--sample-id", "-s", type=click.STRING, required=False)
-def update(id, cohort, patient_id=None, sample_id=None):
-    request = UpdateSampleRequest(
-        patient_id=patient_id,
-        sample_id=sample_id,
-    )
-    return client.sample.update_sample(cohort, id, request)

haplohub_cli-2.5.0/haplohub_cli.egg-info/scm_version.json

@@ -1,8 +0,0 @@
-{
-  "tag": "2.5.0",
-  "distance": 0,
-  "node": "gcd8a204d2e893b5eed8f318fb0e8fb3ed1a25d32",
-  "dirty": false,
-  "branch": "HEAD",
-  "node_date": "2026-07-14"
-}