seer-pas-sdk 0.1.3__py3-none-any.whl → 3.0.0__py3-none-any.whl

seer_pas_sdk-3.0.0.dist-info/RECORD

@@ -0,0 +1,18 @@
+seer_pas_sdk/__init__.py,sha256=Ie6atdmdBV-OmdHHXjhrGhdFGXiyP3JKhKrr3hyvSsA,563
+seer_pas_sdk/auth/__init__.py,sha256=e_eM4jJnnyKUdg4Nggzi9ypt2MLWcEJ8CmCPkUaQDSs,23
+seer_pas_sdk/auth/auth.py,sha256=C9XQWg2dScHcvvypqnjmluRlH-GEuc4D9rYyG9_OnN0,2965
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+seer_pas_sdk/common/errors.py,sha256=4HFORWnaQQCMXRE8kwdsJWvQRB_3KFEZ7yMb391e4gA,142
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+seer_pas_sdk/core/sdk.py,sha256=qYcfBLNwOwgeYgK2Xy9bS26ydqAz9XG778hTbz337Ww,101284
+seer_pas_sdk/core/unsupported.py,sha256=cpWkUXioYEmG7L6GyHZ2Vf-4OfN-UfVX0_KGBAu9jco,59890
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+seer_pas_sdk/objects/groupanalysis.py,sha256=x3D_5NmYBoPDilNCQqUoCFARIfIeUq4FBY3_N6u8tfM,994
+seer_pas_sdk/objects/platemap.py,sha256=8IvJPAecs_e_FyqibzhCw-O4zjCFnf-zMUp_5krTEsg,5864
+seer_pas_sdk/objects/volcanoplot.py,sha256=tKuCWDIdoO8FLJlhpXhuwHn0aMYnvudTugxAslDXyGs,9357
+seer_pas_sdk-3.0.0.dist-info/licenses/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
+seer_pas_sdk-3.0.0.dist-info/METADATA,sha256=WY2yk1sWqKdxg6Ae-5oWFzfSVR1NfL-NCddD-5xLBsU,13448
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+seer_pas_sdk-3.0.0.dist-info/top_level.txt,sha256=-2kZ-KFMGtXwr8H1O5llMKlcJ8gRKohEmrIvazXB61s,13
+seer_pas_sdk-3.0.0.dist-info/RECORD,,

{seer_pas_sdk-0.1.3.dist-info → seer_pas_sdk-3.0.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (73.0.1)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{seer_pas_sdk-0.1.3.dist-info → seer_pas_sdk-3.0.0.dist-info}/top_level.txt

@@ -1,2 +1 @@
 seer_pas_sdk
-tests

seer_pas_sdk-0.1.3.dist-info/METADATA

@@ -1,50 +0,0 @@
-Metadata-Version: 2.1
-Name: seer-pas-sdk
-Version: 0.1.3
-Summary: SDK for Seer Proteograph Analysis Suite (PAS)
-Home-page: https://github.com/seerbio/seer-pas-sdk
-Author: Agam Jolly
-Author-email: ajolly@seer.bio
-Project-URL: Bug Tracker, https://github.com/seerbio/seer-pas-sdk/issues
-Classifier: Programming Language :: Python :: 3
-Classifier: Operating System :: OS Independent
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE.txt
-Requires-Dist: boto3==1.26.152
-Requires-Dist: botocore==1.29.152
-Requires-Dist: pandas==2.0.1
-Requires-Dist: numpy<2.0.0,>=1.5.3
-Requires-Dist: PyJWT==2.8.0
-Requires-Dist: python-dotenv==1.0.0
-Requires-Dist: Requests==2.31.0
-Requires-Dist: tqdm==4.65.0
-
-# Seer PAS Python SDK
-
-[![Test](https://github.com/seerbio/seer-pas-sdk/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/seerbio/seer-pas-sdk/actions/workflows/test.yml)
-[![Lint](https://github.com/seerbio/seer-pas-sdk/actions/workflows/lint.yml/badge.svg?branch=main)](https://github.com/seerbio/seer-pas-sdk/actions/workflows/lint.yml)
-
-This SDK permits interaction with the Seer Proteograph Analysis Suite using Python.
-
-## Installation
-
-```shell
-pip install seer-pas-sdk
-```
-
-## Usage
-
-To import and set up the SDK:
-
-```python
-from seer_pas_sdk import SeerSDK
-
-# Instantiate an SDK object with your credentials:
-sdk = SeerSDK(USERNAME, PASSWORD)
-```
-
-You can then use the SDK's methods to create, query, or retrieve projects, plates, samples, and analyses.
-
-For complete documentation of this SDK, visit [https://seerbio.github.io/seer-pas-sdk/](https://seerbio.github.io/seer-pas-sdk/ "Documentation").

seer_pas_sdk-0.1.3.dist-info/RECORD

@@ -1,19 +0,0 @@
-seer_pas_sdk/__init__.py,sha256=Ie6atdmdBV-OmdHHXjhrGhdFGXiyP3JKhKrr3hyvSsA,563
-seer_pas_sdk/auth/__init__.py,sha256=e_eM4jJnnyKUdg4Nggzi9ypt2MLWcEJ8CmCPkUaQDSs,23
-seer_pas_sdk/auth/auth.py,sha256=DZcbkYel11GvIn-iiutt9UOVfj9URZ_f89QMHhyGfRg,2277
-seer_pas_sdk/common/__init__.py,sha256=QnBup2dT6okt62Yjdhik4DmLf36Ozgv6KybdvFAULaA,12260
-seer_pas_sdk/core/__init__.py,sha256=rxbKgg-Qe24OaxX2zyHHYPYgDCTEKE_-41bB2wvpvL4,25
-seer_pas_sdk/core/sdk.py,sha256=IlTFn09nZ21iHffh502qAvKUhWcO_bcR6c9723AJckw,45291
-seer_pas_sdk/objects/__init__.py,sha256=ljq6G4yeE3GoefDPqEYx1tLrDuD_9H_7_hedo6-OAuk,31
-seer_pas_sdk/objects/platemap.py,sha256=DosquJu2-XvDjVj4JFKoXa0DBVS8OroYCDeS5Np4U8Q,3693
-tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tests/conftest.py,sha256=nu5Qu8CHwgJEwFpLQ0iX8e5csz4HGIC2oe50AdkA2Ms,317
-tests/test_auth.py,sha256=np4XXbEzoSFf-zXKaZQFL4Ry1ehMtjbXtHG3J6D-zzc,933
-tests/test_common.py,sha256=3VgHPbeLVJCh8V0kBGMvkhTKMd6sN_eLJF3AgvbyH0I,3433
-tests/test_objects.py,sha256=BcQtE8CbGUAnFlbkwsaJalUV6D8WbdwN2aWiQddh3k4,2521
-tests/test_sdk.py,sha256=ZNfsRAe_YHIXfteVugfkcds_lmYb0emIfDbJz7jpqR4,239
-seer_pas_sdk-0.1.3.dist-info/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
-seer_pas_sdk-0.1.3.dist-info/METADATA,sha256=3OrGnwgKw2ECRB-LTulbhxFAlbVw7ialPFQdfR39ddg,1714
-seer_pas_sdk-0.1.3.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
-seer_pas_sdk-0.1.3.dist-info/top_level.txt,sha256=gMffZ5LfTF87Sr-oiyl-rtY6omfBslYCA2S4DM7YNC8,19
-seer_pas_sdk-0.1.3.dist-info/RECORD,,

tests/conftest.py

@@ -1,17 +0,0 @@
-"""
-`conftest.py` -- common fixtures and other pytest config
-"""
-
-import pytest
-
-from seer_pas_sdk import PlateMap
-
-
-@pytest.fixture
-def platemap():
-    """A very basic platemap"""
-    return PlateMap(
-        ms_file_name=["test.msfile"],
-        sample_name=["TEST_sample_name"],
-        sample_id=["TEST0"],
-    )

tests/test_auth.py

@@ -1,48 +0,0 @@
-import pytest
-
-from seer_pas_sdk.auth import Auth
-
-
-@pytest.fixture
-def password():
-    return "XXX_fake_password"
-
-
-@pytest.fixture
-def username():
-    return "XXX_fake_user"
-
-
-@pytest.fixture(
-    params=[
-        *Auth._instances.keys(),
-        *Auth._instances.values(),
-        "https://secure-https-url.example/",
-    ]
-)
-def valid_instance(request):
-    return request.param
-
-
-def test_valid_instance(username, password, valid_instance):
-    Auth(
-        username=username,
-        password=password,
-        instance=valid_instance,
-    )
-
-
-@pytest.fixture(
-    params=["XX", "http://insecure-http-url.example/", "my-favorite-instance"]
-)
-def invalid_instance(request):
-    return request.param
-
-
-def test_invalid_instance(username, password, invalid_instance):
-    with pytest.raises(ValueError):
-        Auth(
-            username=username,
-            password=password,
-            instance=invalid_instance,
-        )

tests/test_common.py

@@ -1,99 +0,0 @@
-import pytest
-
-from seer_pas_sdk.common import *
-
-
-@pytest.fixture
-def mock_sample(platemap):
-    """A file name in our mock platemap"""
-    idx = 0
-    return (
-        platemap.ms_file_name[idx],
-        platemap.sample_name[idx],
-        platemap.sample_id[idx],
-    )
-
-
-@pytest.fixture(scope="function")
-def platemap_file(platemap, tmpdir):
-    """Our mock platemap, as a file"""
-    outfile = tmpdir / "test_platemap.csv"
-
-    platemap.to_csv(outfile)
-
-    yield outfile
-
-    # Clean up test file
-    outfile.remove()
-
-
-def test_get_sample_info(platemap_file, mock_sample):
-    """Test that get_sample_info correctly parses the platemap file"""
-    filename, sample_name, sample_id = mock_sample
-
-    plate_id = "TEST_plate_id"
-    ms_data_files = {filename}
-    space = "TEST_space_id"
-    res = get_sample_info(
-        plate_id=plate_id,
-        ms_data_files=ms_data_files,
-        plate_map_file=platemap_file,
-        space=space,
-        sample_description_file=None,  # TODO: test sample description file
-    )
-
-    assert len(res) == 1
-
-    for sampleinfo in res:
-        assert sampleinfo["plateID"] == plate_id
-        assert sampleinfo["sampleName"] == sample_name
-        assert sampleinfo["sampleID"] == sample_id
-        assert sampleinfo["sampleUserGroup"] == space
-
-
-def test_get_sample_info_missing_file(platemap_file):
-    """Test that get_sample_info raises an exception if a file doesn't exist"""
-
-    plate_id = "TEST_plate_id"
-    ms_data_files = {"XXX_file_does_not_exist"}
-    space = "TEST_space_id"
-    with pytest.raises(ValueError):
-        res = get_sample_info(
-            plate_id=plate_id,
-            ms_data_files=ms_data_files,
-            plate_map_file=platemap_file,
-            space=space,
-        )
-
-
-def test_camel_case():
-    assert camel_case("my favorite") == "myFavorite"
-    assert camel_case("my Favorite") == "myFavorite"
-    assert camel_case("My favorite") == "myFavorite"
-    assert camel_case("My Favorite") == "myFavorite"
-    assert camel_case("snake_case") == "snakeCase"
-    assert camel_case("snake_Case") == "snakeCase"
-    assert camel_case("Snake_case") == "snakeCase"
-    assert camel_case("Snake_Case") == "snakeCase"
-    assert camel_case("camelcase") == "camelcase"
-    assert camel_case("camelCase") == "camelcase"
-    assert camel_case("Camelcase") == "camelcase"
-    assert camel_case("CamelCase") == "camelcase"
-    assert camel_case("kebab-case") == "kebabCase"
-    assert camel_case("kebab-Case") == "kebabCase"
-    assert camel_case("Kebab-case") == "kebabCase"
-    assert camel_case("Kebab-Case") == "kebabCase"
-
-    # Corner cases:
-    assert camel_case("two\nlines") == "two\nLines"
-    assert camel_case("two\nLines") == "two\nLines"
-    assert camel_case("Two\nlines") == "two\nLines"
-    assert camel_case("Two\nLines") == "two\nLines"
-    assert camel_case("über コンピュータコード") == "überコンピュータコード"
-    assert camel_case("über コンピュータコード") == "überコンピュータコード"
-    assert camel_case("Über コンピュータコード") == "überコンピュータコード"
-    assert camel_case("Über コンピュータコード") == "überコンピュータコード"
-    assert camel_case("clap👏back") == "clap👏Back"
-    assert camel_case("clap👏Back") == "clap👏Back"
-    assert camel_case("Clap👏back") == "clap👏Back"
-    assert camel_case("Clap👏Back") == "clap👏Back"

tests/test_objects.py

@@ -1,91 +0,0 @@
-from io import StringIO
-
-import pandas as pd
-import pytest
-
-from seer_pas_sdk.objects import PlateMap
-
-
-def test_toofew_items():
-    """Test passing too few items to one or more attributes"""
-    filenames = ["test_0.msfile", "test_1.msfile"]
-    samplenames = ["TEST_sample_name"]
-    platemap = PlateMap(
-        ms_file_name=filenames.copy(),  # prevent mutating shared state
-        sample_name=samplenames.copy(),  # prevent mutating shared state
-    )
-
-    assert len(platemap.ms_file_name) == len(filenames)
-    assert len(platemap.sample_name) == len(filenames)
-
-    for i in range(len(platemap.sample_name)):
-        assert (platemap.sample_name[i] == None) == (i >= len(samplenames))
-
-
-def test_toomany_items():
-    with pytest.raises(ValueError):
-        PlateMap(
-            ms_file_name=["test.msfile"],
-            sample_name=["TEST_sample_name_0", "TEST_sample_name_1"],
-        )
-
-
-def test_platemap_to_dict(platemap):
-    res = platemap.to_dict()
-
-    assert isinstance(res, dict)
-
-    for k in res:
-        assert len(res[k]) == platemap.length
-
-
-def test_platemap_to_df(platemap):
-    res = platemap.to_df()
-
-    assert isinstance(res, pd.DataFrame)
-
-    assert len(res) == platemap.length
-
-    for k in res.columns:
-        assert len(res[k]) == platemap.length
-
-
-def test_platemap_to_csv_str(platemap):
-    res = platemap.to_csv()
-
-    assert isinstance(res, str)
-    assert len(StringIO(res).readlines()) == platemap.length + 1
-
-    # Re-parse CSV with Pandas for additional checks
-    df = pd.read_csv(StringIO(res))
-
-    assert len(df) == platemap.length
-    for k in df.columns:
-        assert len(df[k]) == platemap.length
-
-
-def test_platemap_to_csv_file(platemap, tmpdir):
-    outfile = tmpdir / "test.csv"
-    res = platemap.to_csv(outfile)
-
-    with open(outfile, "r") as f:
-        assert len(f.readlines()) == platemap.length + 1
-
-        # Re-parse CSV with Pandas for additional checks
-        f.seek(0)
-        df = pd.read_csv(f)
-
-    assert len(df) == platemap.length
-    for k in df.columns:
-        assert len(df[k]) == platemap.length
-
-
-def test_mutate_defaults():
-    """Test that default values in the construtor aren't shared mutable instances"""
-
-    # Force extension of default (empty) values by creating a platemap with 2 samples
-    platemap_0 = PlateMap(["test_0.msfile", "test_1.msfile"])
-
-    # Now create a platemap with fewer samples; this will trigger an error if the default
-    # values were mutated by the first call.
-    platemap_1 = PlateMap(["test_0.msfile"])

tests/test_sdk.py

@@ -1,11 +0,0 @@
-"""
-`test_sdk` -- high-level tests for the seer-pas-sdk package
-"""
-
-
-def test_import():
-    """
-    Stub test that importing the root module is successful.
-    TODO: replace this with more meaningful tests
-    """
-    import seer_pas_sdk