biolmai 0.1.5__py2.py3-none-any.whl → 0.1.7__py2.py3-none-any.whl

biolmai/auth.py

@@ -6,20 +6,19 @@ import stat
 import click
 import requests
 
-from biolmai.const import ACCESS_TOK_PATH, BASE_DOMAIN, GEN_TOKEN_URL, \
-    USER_BIOLM_DIR
+from biolmai.const import ACCESS_TOK_PATH, BASE_DOMAIN, GEN_TOKEN_URL, USER_BIOLM_DIR
 
 
 def validate_user_auth(api_token=None, access=None, refresh=None):
     """Validates an API token, to be used as 'Authorization: Token 1235abc'
     authentication method."""
-    url = f'{BASE_DOMAIN}/api/v1/auth/login-check/'
+    url = f"{BASE_DOMAIN}/api/v1/auth/login-check/"
     if api_token is not None:
-        headers = {'Authorization': f'Token {api_token}'}
+        headers = {"Authorization": f"Token {api_token}"}
     else:
         headers = {
-            'Cookie': 'access={};refresh={}'.format(access, refresh),
-            'Content-Type': 'application/json'
+            "Cookie": f"access={access};refresh={refresh}",
+            "Content-Type": "application/json",
         }
     try:
         r = requests.post(url=url, headers=headers)
@@ -36,28 +35,25 @@ def validate_user_auth(api_token=None, access=None, refresh=None):
 def refresh_access_token(refresh):
     """Attempt to refresh temporary user access token, by using their refresh
     token, which has a longer TTL."""
-    url = f'{BASE_DOMAIN}/api/auth/token/refresh/'
-    headers = {
-        'Cookie': 'refresh={}'.format(refresh),
-        'Content-Type': 'application/json'
-    }
+    url = f"{BASE_DOMAIN}/api/auth/token/refresh/"
+    headers = {"Cookie": f"refresh={refresh}", "Content-Type": "application/json"}
     r = requests.post(url=url, headers=headers)
     json_response = r.json()
-    if r.status_code != 200 or (r.status_code == 200 and 'code' in r.json()):
+    if r.status_code != 200 or (r.status_code == 200 and "code" in r.json()):
         pretty_json = pprint.pformat(json_response, indent=2)
         click.echo(pretty_json)
-        click.echo(f"Token refresh failed! Please login by "
-                   "running `biolmai login`.\n")
+        click.echo(
+            "Token refresh failed! Please login by " "running `biolmai login`.\n"
+        )
         return False
     else:
-        access_refresh_dict = {'access': json_response['access'],
-                               'refresh': refresh}
+        access_refresh_dict = {"access": json_response["access"], "refresh": refresh}
         save_access_refresh_token(access_refresh_dict)
         return True
 
 
 def get_auth_status():
-    environ_token = os.environ.get('BIOLMAI_TOKEN', None)
+    environ_token = os.environ.get("BIOLMAI_TOKEN", None)
     if environ_token:
         msg = "Environment variable BIOLMAI_TOKEN detected. Validating token..."
         click.echo(msg)
@@ -65,12 +61,14 @@ def get_auth_status():
     elif os.path.exists(ACCESS_TOK_PATH):
         msg = f"Credentials file found {ACCESS_TOK_PATH}. Validating token..."
         click.echo(msg)
-        with open(ACCESS_TOK_PATH, 'r') as f:
+        with open(ACCESS_TOK_PATH) as f:
             access_refresh_dict = json.load(f)
-        access = access_refresh_dict.get('access')
-        refresh = access_refresh_dict.get('refresh')
+        access = access_refresh_dict.get("access")
+        refresh = access_refresh_dict.get("refresh")
         resp = validate_user_auth(access=access, refresh=refresh)
-        if resp.status_code != 200 or (resp.status_code == 200 and 'code' in resp.json()):
+        if resp.status_code != 200 or (
+            resp.status_code == 200 and "code" in resp.json()
+        ):
             click.echo("Access token validation failed. Attempting to refresh token...")
             # Attempt to use the 'refresh' token to get a new 'access' token
             if not refresh_access_token(refresh):
@@ -78,9 +76,11 @@ def get_auth_status():
             else:
                 click.echo("Access token refresh was successful.")
     else:
-        msg = f"No https://biolm.ai credentials found. Please " \
-              f"set the environment variable BIOLMAI_TOKEN to a token from {GEN_TOKEN_URL}, or login by " \
-              "running `biolmai login`."
+        msg = (
+            f"No https://biolm.ai credentials found. Please "
+            f"set the environment variable BIOLMAI_TOKEN to a token from "
+            f"{GEN_TOKEN_URL}, or login by running `biolmai login`."
+        )
         click.echo(msg)
 
 
@@ -95,9 +95,9 @@ def generate_access_token(uname, password):
     more permanent auth method for the API, use an API token by setting the
     BIOLMAI_TOKEN environment variable.
     """
-    url = f'{BASE_DOMAIN}/api/auth/token/'
+    url = f"{BASE_DOMAIN}/api/auth/token/"
     try:
-        r = requests.post(url=url, data={'username': uname, 'password': password})
+        r = requests.post(url=url, data={"username": uname, "password": password})
         json_response = r.json()
     except Exception:
         click.echo("Login failed!\n")
@@ -118,12 +118,12 @@ def save_access_refresh_token(access_refresh_dict):
     use."""
     os.makedirs(USER_BIOLM_DIR, exist_ok=True)
     # Save token
-    with open(ACCESS_TOK_PATH, 'w') as f:
+    with open(ACCESS_TOK_PATH, "w") as f:
         json.dump(access_refresh_dict, f)
     os.chmod(ACCESS_TOK_PATH, stat.S_IRUSR | stat.S_IWUSR)
     # Validate token and print user info
-    access = access_refresh_dict.get('access')
-    refresh = access_refresh_dict.get('refresh')
+    access = access_refresh_dict.get("access")
+    refresh = access_refresh_dict.get("refresh")
     validate_user_auth(access=access, refresh=refresh)
 
 
@@ -134,13 +134,13 @@ def get_api_token():
     """
     url = "https://biolm.ai/api/auth/token/"
 
-    payload = json.dumps({
-        "username": os.environ.get("BIOLM_USER"),
-        "password": os.environ.get("BIOLM_PASSWORD")
-    })
-    headers = {
-        'Content-Type': 'application/json'
-    }
+    payload = json.dumps(
+        {
+            "username": os.environ.get("BIOLM_USER"),
+            "password": os.environ.get("BIOLM_PASSWORD"),
+        }
+    )
+    headers = {"Content-Type": "application/json"}
 
     response = requests.request("POST", url, headers=headers, data=payload)
     response_json = response.json()
@@ -152,19 +152,22 @@ def get_user_auth_header():
     """Returns a dict with the appropriate Authorization header, either using
     an API token from BIOLMAI_TOKEN environment variable, or by reading the
     credentials file at ~/.biolmai/credntials next."""
-    api_token = os.environ.get('BIOLMAI_TOKEN', None)
+    api_token = os.environ.get("BIOLMAI_TOKEN", None)
     if api_token:
-        headers = {'Authorization': f'Token {api_token}'}
+        headers = {"Authorization": f"Token {api_token}"}
     elif os.path.exists(ACCESS_TOK_PATH):
-        with open(ACCESS_TOK_PATH, 'r') as f:
+        with open(ACCESS_TOK_PATH) as f:
             access_refresh_dict = json.load(f)
-        access = access_refresh_dict.get('access')
-        refresh = access_refresh_dict.get('refresh')
+        access = access_refresh_dict.get("access")
+        refresh = access_refresh_dict.get("refresh")
         headers = {
-            'Cookie': 'access={};refresh={}'.format(access, refresh),
-            'Content-Type': 'application/json'
+            "Cookie": f"access={access};refresh={refresh}",
+            "Content-Type": "application/json",
         }
     else:
-        err = "No https://biolm.ai credentials found. Please run `biolmai status` to debug."
+        err = (
+            "No https://biolm.ai credentials found. Please run "
+            "`biolmai status` to debug."
+        )
         raise AssertionError(err)
     return headers

biolmai/biolmai.py

@@ -2,6 +2,4 @@
 
 import logging
 
-log = logging.getLogger('biolm_util')
-
-
+log = logging.getLogger("biolm_util")

biolmai/cli.py

@@ -1,37 +1,43 @@
 """Console script for biolmai."""
+import os
 import sys
+
 import click
-import os
-from biolmai.auth import generate_access_token, \
-    get_auth_status, save_access_refresh_token
-from biolmai.const import ACCESS_TOK_PATH, MULTIPROCESS_THREADS, BASE_API_URL
+
+from biolmai.auth import (
+    generate_access_token,
+    get_auth_status,
+    save_access_refresh_token,
+)
+from biolmai.const import ACCESS_TOK_PATH, BASE_API_URL, MULTIPROCESS_THREADS
 
 
 @click.command()
 def main(args=None):
     """Console script for biolmai."""
-    click.echo("Replace this message by putting your code into "
-               "biolmai.cli.main")
+    click.echo("Replace this message by putting your code into " "biolmai.cli.main")
     click.echo("See click documentation at https://click.palletsprojects.com/")
     return 0
 
 
 @click.group()
-@click.option('--debug/--no-debug', default=False)
+@click.option("--debug/--no-debug", default=False)
 def cli(debug):
     pass
 
 
 def echo_env_vars():
-    env_var_tok = os.environ.get('BIOLMAI_TOKEN', '')[:6]
+    env_var_tok = os.environ.get("BIOLMAI_TOKEN", "")[:6]
     if env_var_tok and len(env_var_tok) == 6:
-        env_var_tok += '*****************'
-    s = '\n'.join([
-        "BIOLMAI_TOKEN={}".format(env_var_tok),
-        f"BIOLMAI_ACCESS_CRED={ACCESS_TOK_PATH}",
-        "BIOLMAI_THREADS={}".format(MULTIPROCESS_THREADS or ''),
-        f"BIOLMAI_BASE_API_URL={BASE_API_URL}"
-    ])
+        env_var_tok += "*****************"
+    s = "\n".join(
+        [
+            f"BIOLMAI_TOKEN={env_var_tok}",
+            f"BIOLMAI_ACCESS_CRED={ACCESS_TOK_PATH}",
+            "BIOLMAI_THREADS={}".format(MULTIPROCESS_THREADS or ""),
+            f"BIOLMAI_BASE_API_URL={BASE_API_URL}",
+        ]
+    )
     click.echo(s)
 
 
@@ -43,17 +49,19 @@ def status():
 
 @cli.command()
 def login():
-    uname = click.prompt("Username", default=None, hide_input=False,
-                  confirmation_prompt=False, type=str)
-    password = click.prompt("Password", default=None, hide_input=True,
-                  confirmation_prompt=False, type=str)
+    uname = click.prompt(
+        "Username", default=None, hide_input=False, confirmation_prompt=False, type=str
+    )
+    password = click.prompt(
+        "Password", default=None, hide_input=True, confirmation_prompt=False, type=str
+    )
     access_refresh_tok_dict = generate_access_token(uname, password)
     try:
-        access = access_refresh_tok_dict.get('access')
-        refresh = access_refresh_tok_dict.get('refresh')
+        assert access_refresh_tok_dict.get("access") is not None
+        assert access_refresh_tok_dict.get("refresh") is not None
         click.echo("Saving new access and refresh token.")
         save_access_refresh_token(access_refresh_tok_dict)
-    except Exception as e:
+    except Exception:
         click.echo("Unhandled login exception!")
         raise
 

biolmai/cls.py

@@ -1,19 +1,19 @@
 """API inference classes."""
-from biolmai.api import APIEndpoint, PredictAction, TransformAction, GenerateAction
-from biolmai.validate import UnambiguousAA, ExtendedAAPlusExtra, SingleOccurrenceOf
+from biolmai.api import APIEndpoint, GenerateAction, PredictAction, TransformAction
+from biolmai.validate import ExtendedAAPlusExtra, SingleOccurrenceOf, UnambiguousAA
 
 
 class ESMFoldSingleChain(APIEndpoint):
-    slug = 'esmfold-singlechain'
-    action_classes = (PredictAction, )
-    seq_classes = (UnambiguousAA(), )
+    slug = "esmfold-singlechain"
+    action_classes = (PredictAction,)
+    seq_classes = (UnambiguousAA(),)
     batch_size = 2
 
 
 class ESMFoldMultiChain(APIEndpoint):
-    slug = 'esmfold-multichain'
-    action_classes = (PredictAction, )
-    seq_classes = (ExtendedAAPlusExtra(extra=[':']), )
+    slug = "esmfold-multichain"
+    action_classes = (PredictAction,)
+    seq_classes = (ExtendedAAPlusExtra(extra=[":"]),)
     batch_size = 2
 
 
@@ -29,9 +29,10 @@ class ESM2Embeddings(APIEndpoint):
          }]
        }
     """
-    slug = 'esm2_t33_650M_UR50D'
+
+    slug = "esm2_t33_650M_UR50D"
     action_classes = (TransformAction,)
-    seq_classes = (UnambiguousAA(), )
+    seq_classes = (UnambiguousAA(),)
     batch_size = 1
 
 
@@ -47,54 +48,50 @@ class ESM1v1(APIEndpoint):
           }]
        }
     """
-    slug = 'esm1v_t33_650M_UR90S_1'
-    action_classes = (PredictAction, )
-    seq_classes = (SingleOccurrenceOf('<mask>'),
-                   ExtendedAAPlusExtra(extra=['<mask>']))
+
+    slug = "esm1v_t33_650M_UR90S_1"
+    action_classes = (PredictAction,)
+    seq_classes = (SingleOccurrenceOf("<mask>"), ExtendedAAPlusExtra(extra=["<mask>"]))
     batch_size = 5
 
 
 class ESM1v2(APIEndpoint):
-    slug = 'esm1v_t33_650M_UR90S_2'
-    action_classes = (PredictAction, )
-    seq_classes = (SingleOccurrenceOf('<mask>'),
-                   ExtendedAAPlusExtra(extra=['<mask>']))
+    slug = "esm1v_t33_650M_UR90S_2"
+    action_classes = (PredictAction,)
+    seq_classes = (SingleOccurrenceOf("<mask>"), ExtendedAAPlusExtra(extra=["<mask>"]))
     batch_size = 5
 
 
 class ESM1v3(APIEndpoint):
-    slug = 'esm1v_t33_650M_UR90S_3'
-    action_classes = (PredictAction, )
-    seq_classes = (SingleOccurrenceOf('<mask>'),
-                   ExtendedAAPlusExtra(extra=['<mask>']))
+    slug = "esm1v_t33_650M_UR90S_3"
+    action_classes = (PredictAction,)
+    seq_classes = (SingleOccurrenceOf("<mask>"), ExtendedAAPlusExtra(extra=["<mask>"]))
     batch_size = 5
 
 
 class ESM1v4(APIEndpoint):
-    slug = 'esm1v_t33_650M_UR90S_4'
-    action_classes = (PredictAction, )
-    seq_classes = (SingleOccurrenceOf('<mask>'),
-                   ExtendedAAPlusExtra(extra=['<mask>']))
+    slug = "esm1v_t33_650M_UR90S_4"
+    action_classes = (PredictAction,)
+    seq_classes = (SingleOccurrenceOf("<mask>"), ExtendedAAPlusExtra(extra=["<mask>"]))
     batch_size = 5
 
 
 class ESM1v5(APIEndpoint):
-    slug = 'esm1v_t33_650M_UR90S_5'
-    action_classes = (PredictAction, )
-    seq_classes = (SingleOccurrenceOf('<mask>'),
-                   ExtendedAAPlusExtra(extra=['<mask>']))
+    slug = "esm1v_t33_650M_UR90S_5"
+    action_classes = (PredictAction,)
+    seq_classes = (SingleOccurrenceOf("<mask>"), ExtendedAAPlusExtra(extra=["<mask>"]))
     batch_size = 5
 
 
 class ESMIF1(APIEndpoint):
-    slug = 'esmif1'
-    action_classes = (GenerateAction, )
-    seq_classes = tuple([])
+    slug = "esmif1"
+    action_classes = (GenerateAction,)
+    seq_classes = ()
     batch_size = 2
 
 
 class Progen2(APIEndpoint):
-    slug = 'progen2'
-    action_classes = (GenerateAction, )
-    seq_classes = tuple([])
+    slug = "progen2"
+    action_classes = (GenerateAction,)
+    seq_classes = ()
     batch_size = 1

biolmai/const.py

@@ -1,27 +1,29 @@
-import os
 import multiprocessing
+import os
 
 cpu_count = multiprocessing.cpu_count()
 max_threads = cpu_count * 4
 
-if os.environ.get('BIOLMAI_LOCAL', False):
+if os.environ.get("BIOLMAI_LOCAL", False):
     # For local development and tests only
-    BASE_DOMAIN = 'http://localhost:8000'
+    BASE_DOMAIN = "http://localhost:8000"
 else:
-    BASE_DOMAIN = 'https://biolm.ai'
+    BASE_DOMAIN = "https://biolm.ai"
 
-USER_BIOLM_DIR = os.path.join(os.path.expanduser('~'), '.biolmai')
-ACCESS_TOK_PATH = os.path.join(USER_BIOLM_DIR, 'credentials')
-GEN_TOKEN_URL = f'{BASE_DOMAIN}/ui/accounts/user-api-tokens/'
-MULTIPROCESS_THREADS = os.environ.get('BIOLMAI_THREADS', 1)
+USER_BIOLM_DIR = os.path.join(os.path.expanduser("~"), ".biolmai")
+ACCESS_TOK_PATH = os.path.join(USER_BIOLM_DIR, "credentials")
+GEN_TOKEN_URL = f"{BASE_DOMAIN}/ui/accounts/user-api-tokens/"
+MULTIPROCESS_THREADS = os.environ.get("BIOLMAI_THREADS", 1)
 if isinstance(MULTIPROCESS_THREADS, str) and not MULTIPROCESS_THREADS:
     MULTIPROCESS_THREADS = 1
 if int(MULTIPROCESS_THREADS) > max_threads or int(MULTIPROCESS_THREADS) > 128:
-    err = f"Maximum threads allowed is 4x number of CPU cores (" \
-          f"{max_threads}) or 128, whichever is lower."
+    err = (
+        f"Maximum threads allowed is 4x number of CPU cores ("
+        f"{max_threads}) or 128, whichever is lower."
+    )
     err += " Please update environment variable BIOLMAI_THREADS."
     raise ValueError(err)
 elif int(MULTIPROCESS_THREADS) <= 0:
     err = "Environment variable BIOLMAI_THREADS must be a positive integer."
     raise ValueError(err)
-BASE_API_URL = f'{BASE_DOMAIN}/api/v1'
+BASE_API_URL = f"{BASE_DOMAIN}/api/v1"

biolmai/payloads.py

@@ -1,29 +1,28 @@
 def INST_DAT_TXT(batch, include_batch_size=False):
     d = {"instances": []}
-    for idx, row in batch.iterrows():
+    for _, row in batch.iterrows():
         inst = {"data": {"text": row.text}}
-        d['instances'].append(inst)
+        d["instances"].append(inst)
     if include_batch_size is True:
-        d['batch_size'] = len(d['instances'])
+        d["batch_size"] = len(d["instances"])
     return d
 
 
-def predict_resp_many_in_one_to_many_singles(resp_json, status_code,
-                                             batch_id, local_err, batch_size):
-    expected_root_key = 'predictions'
+def predict_resp_many_in_one_to_many_singles(
+    resp_json, status_code, batch_id, local_err, batch_size
+):
+    expected_root_key = "predictions"
     to_ret = []
     if not local_err and status_code and status_code == 200:
         list_of_individual_seq_results = resp_json[expected_root_key]
     elif local_err:
-        list_of_individual_seq_results = [{'error': resp_json}]
+        list_of_individual_seq_results = [{"error": resp_json}]
     elif status_code and status_code != 200 and isinstance(resp_json, dict):
         list_of_individual_seq_results = [resp_json] * batch_size
     else:
         raise ValueError("Unexpected response in parser")
     for idx, item in enumerate(list_of_individual_seq_results):
-        d = {'status_code': status_code,
-             'batch_id': batch_id,
-             'batch_item': idx}
+        d = {"status_code": status_code, "batch_id": batch_id, "batch_item": idx}
         if not status_code or status_code != 200:
             d.update(item)  # Put all resp keys at root there
         else:

biolmai/validate.py

@@ -1,28 +1,47 @@
 import re
 
-UNAMBIGUOUS_AA = ('A', 'C', 'D', 'E', 'F', 'G', 'H',
-                  'I', 'K', 'L', 'M', 'N', 'P', 'Q',
-                  'R', 'S', 'T', 'V', 'W', 'Y' )
-AAs = ''.join(UNAMBIGUOUS_AA)
+UNAMBIGUOUS_AA = (
+    "A",
+    "C",
+    "D",
+    "E",
+    "F",
+    "G",
+    "H",
+    "I",
+    "K",
+    "L",
+    "M",
+    "N",
+    "P",
+    "Q",
+    "R",
+    "S",
+    "T",
+    "V",
+    "W",
+    "Y",
+)
+AAs = "".join(UNAMBIGUOUS_AA)
 # Let's use extended list for ESM-1v
-AAs_EXTENDED = 'ACDEFGHIKLMNPQRSTVWYBXZJUO'
+AAs_EXTENDED = "ACDEFGHIKLMNPQRSTVWYBXZJUO"
 
 
-UNAMBIGUOUS_DNA = ('A', 'C', 'T', 'G')
-AMBIGUOUS_DNA = ('A', 'C', 'T', 'G', 'X', 'N', 'U')
+UNAMBIGUOUS_DNA = ("A", "C", "T", "G")
+AMBIGUOUS_DNA = ("A", "C", "T", "G", "X", "N", "U")
 
 
 regexes = {
-    'empty_or_unambiguous_aa_validator': re.compile(f"^[{AAs}]*$"),
-    'empty_or_unambiguous_dna_validator': re.compile(r"^[ACGT]*$"),
-    'extended_aa_validator': re.compile(f"^[{AAs_EXTENDED}]+$"),
-    'unambiguous_aa_validator': re.compile(f"^[{AAs}]+$"),
-    'unambiguous_dna_validator': re.compile(r"^[ACGT]+$"),
+    "empty_or_unambiguous_aa_validator": re.compile(f"^[{AAs}]*$"),
+    "empty_or_unambiguous_dna_validator": re.compile(r"^[ACGT]*$"),
+    "extended_aa_validator": re.compile(f"^[{AAs_EXTENDED}]+$"),
+    "unambiguous_aa_validator": re.compile(f"^[{AAs}]+$"),
+    "unambiguous_dna_validator": re.compile(r"^[ACGT]+$"),
 }
 
 
 def empty_or_unambiguous_aa_validator(txt):
-    r = regexes['empty_or_unambiguous_aa_validator']
+    r = regexes["empty_or_unambiguous_aa_validator"]
     if not bool(r.match(txt)):
         err = f"Residues can only be represented with '{AAs}' characters"
         raise AssertionError(err)
@@ -30,36 +49,40 @@ def empty_or_unambiguous_aa_validator(txt):
 
 
 def empty_or_unambiguous_dna_validator(txt):
-    r = regexes['empty_or_unambiguous_dna_validator']
+    r = regexes["empty_or_unambiguous_dna_validator"]
     if not bool(r.match(txt)):
-        err = f"Nucleotides can only be represented with 'ACTG' characters"
+        err = "Nucleotides can only be represented with 'ACTG' characters"
         raise AssertionError(err)
     return txt
 
 
 def extended_aa_validator(txt):
-    r = regexes['extended_aa_validator']
+    r = regexes["extended_aa_validator"]
     if not bool(r.match(txt)):
-        err = f"Extended residues can only be represented with " \
-              f"'{AAs_EXTENDED}' characters"
+        err = (
+            f"Extended residues can only be represented with "
+            f"'{AAs_EXTENDED}' characters"
+        )
         raise AssertionError(err)
     return txt
 
 
 def unambiguous_aa_validator(txt):
-    r = regexes['unambiguous_aa_validator']
+    r = regexes["unambiguous_aa_validator"]
     if not bool(r.match(txt)):
-        err = f"Unambiguous residues can only be represented with '{AAs}' " \
-              f"characters"
+        err = (
+            f"Unambiguous residues can only be represented with '{AAs}' " f"characters"
+        )
         raise AssertionError(err)
     return txt
 
 
 def unambiguous_dna_validator(txt):
-    r = regexes['unambiguous_dna_validator']
+    r = regexes["unambiguous_dna_validator"]
     if not bool(r.match(txt)):
-        err = f"Unambiguous nucleotides can only be represented with 'ACTG' " \
-              f"characters"
+        err = (
+            "Unambiguous nucleotides can only be represented with 'ACTG' " "characters"
+        )
         raise AssertionError(err)
     return txt
 
@@ -70,7 +93,9 @@ class UnambiguousAA:
 
 
 class UnambiguousAAPlusExtra:
-    def __init__(self, extra=[]):
+    def __init__(self, extra=None):
+        if extra is None:
+            extra = []
         self.extra = extra
         assert len(extra) > 0
         assert isinstance(extra, list)
@@ -78,12 +103,14 @@ class UnambiguousAAPlusExtra:
     def __call__(self, value):
         txt_clean = value
         for ex in self.extra:
-            txt_clean = value.replace(ex, '')
+            txt_clean = value.replace(ex, "")
         _ = unambiguous_aa_validator(txt_clean)
 
 
 class ExtendedAAPlusExtra:
-    def __init__(self, extra=[]):
+    def __init__(self, extra=None):
+        if extra is None:
+            extra = []
         self.extra = extra
         assert len(extra) > 0
         assert isinstance(extra, list)
@@ -91,7 +118,7 @@ class ExtendedAAPlusExtra:
     def __call__(self, value):
         txt_clean = value
         for ex in self.extra:
-            txt_clean = value.replace(ex, '')
+            txt_clean = value.replace(ex, "")
         _ = extended_aa_validator(txt_clean)
 
 

{biolmai-0.1.5.dist-info → biolmai-0.1.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biolmai
-Version: 0.1.5
+Version: 0.1.7
 Summary: Python client and SDK for https://biolm.ai
 Home-page: https://github.com/BioLM/py-biolm
 Author: Nikhil Haas

biolmai-0.1.7.dist-info/RECORD

@@ -0,0 +1,18 @@
+biolmai/__init__.py,sha256=lJ7PiA_IyjKhz3dI8nrnqy8S_wqAHtEM3iN3v3eArr0,136
+biolmai/api.py,sha256=3DcXeTFwXdn2KpHrGPxFGN6bvzdFjK6_4KUZuaRe64w,10974
+biolmai/asynch.py,sha256=ZLCiNdGDR2XvijM6jFB2IFl3bG7ROp4PxKbo1rI5s7A,8698
+biolmai/auth.py,sha256=flI9KAD90qdXyLDnpJTrc9voKsiK0uWtD2ehsPBn8r4,6329
+biolmai/biolmai.py,sha256=xwjAvuw6AtmQdkRf_usSGUZ-k2oU-fjl82_WAgfSvVE,74
+biolmai/cli.py,sha256=bdb4q8QlN73A6Ttz0e-dBIwoct7PYqy5WSc52jCMIyU,1967
+biolmai/cls.py,sha256=yacZIwDyDq3sgU3FSc-l8uld83lkwSTh4wiS-vGNT4I,2425
+biolmai/const.py,sha256=kbpmBEm-bw7lhGIJcMFeq1pfsIYeRk01_JwBufjupXc,1111
+biolmai/ltc.py,sha256=al7HZc5tLyUR5fmpIb95hOz5ctudVsc0xzjd_c2Ew3M,49
+biolmai/payloads.py,sha256=WmFN9JUojbrdvd_By8WWURS6Gm5Bh1fPYK0UjLDCbzU,1356
+biolmai/validate.py,sha256=QdPDuZodHn85p1Y7KGkxCDMuRcXBOzAB9lkNZpigw9g,3311
+biolmai-0.1.7.dist-info/AUTHORS.rst,sha256=TB_ACuFPgVmxn1NspYwksTdT6jdZeShcxfafmi-XWKQ,158
+biolmai-0.1.7.dist-info/LICENSE,sha256=8yt0SdP38I7a3g0zWqZjNe0VSDQhJA4bWLQSqqKtAVg,583
+biolmai-0.1.7.dist-info/METADATA,sha256=S2JBm8gzzRm_Xsb0aY3LozcW9TSocbqFLZd8BsA7gQw,1929
+biolmai-0.1.7.dist-info/WHEEL,sha256=bb2Ot9scclHKMOLDEHY6B2sicWOgugjFKaJsT7vwMQo,110
+biolmai-0.1.7.dist-info/entry_points.txt,sha256=ylQnDpCYrxF1F9z_T7NRQcYMWYF5ia_KsTUuboxjEAM,44
+biolmai-0.1.7.dist-info/top_level.txt,sha256=jyQO45JN3g_jbdI8WqMnb0aEIzf4h1MrmPAZkKgfnwY,8
+biolmai-0.1.7.dist-info/RECORD,,

{biolmai-0.1.5.dist-info → biolmai-0.1.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.0)
+Generator: bdist_wheel (0.38.4)
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any