biolmai 0.1.4__py2.py3-none-any.whl → 0.1.7__py2.py3-none-any.whl

biolmai/cls.py

@@ -1 +1,97 @@
 """API inference classes."""
+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(),)
+    batch_size = 2
+
+
+class ESMFoldMultiChain(APIEndpoint):
+    slug = "esmfold-multichain"
+    action_classes = (PredictAction,)
+    seq_classes = (ExtendedAAPlusExtra(extra=[":"]),)
+    batch_size = 2
+
+
+class ESM2Embeddings(APIEndpoint):
+    """Example.
+
+    .. highlight:: python
+    .. code-block:: python
+
+       {
+         "instances": [{
+           "data": {"text": "MSILVTRPSPAGEELVSRLRTLGQVAWHFPLIEFSPGQQLPQ"}
+         }]
+       }
+    """
+
+    slug = "esm2_t33_650M_UR50D"
+    action_classes = (TransformAction,)
+    seq_classes = (UnambiguousAA(),)
+    batch_size = 1
+
+
+class ESM1v1(APIEndpoint):
+    """Example.
+
+    .. highlight:: python
+    .. code-block:: python
+
+       {
+          "instances": [{
+            "data": {"text": "QERLEUTGR<mask>SLGYNIVAT"}
+          }]
+       }
+    """
+
+    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>"]))
+    batch_size = 5
+
+
+class ESM1v3(APIEndpoint):
+    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>"]))
+    batch_size = 5
+
+
+class ESM1v5(APIEndpoint):
+    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 = ()
+    batch_size = 2
+
+
+class Progen2(APIEndpoint):
+    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

@@ -1,8 +1,33 @@
 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"
+    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}]
+    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}
+        if not status_code or status_code != 200:
+            d.update(item)  # Put all resp keys at root there
+        else:
+            # We just append one item, mimicking a single seq in POST req/resp
+            d[expected_root_key] = []
+            d[expected_root_key].append(item)
+        to_ret.append(d)
+    return to_ret

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-0.1.4.dist-info → biolmai-0.1.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biolmai
-Version: 0.1.4
+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-0.1.4.dist-info → biolmai-0.1.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.40.0)
+Generator: bdist_wheel (0.38.4)
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any

biolmai-0.1.4.dist-info/RECORD

@@ -1,18 +0,0 @@
-biolmai/__init__.py,sha256=fbDI9cxEz865hVVZpWg5XWv546aL98bt9s9Xe1r_v74,340
-biolmai/api.py,sha256=3XEJ_AIBqe0FBGmEtD85w_uVZs1D8v2nfviC0KKlUQY,13513
-biolmai/asynch.py,sha256=R6p_i-1KK7xGmw1EPUCUYRiwg2tyl-D2JkaNUvUYL3w,7455
-biolmai/auth.py,sha256=Z1lCrN4xJjf5dP7tMxQ0O7cQ7BomwhTdjp4c2NwQuIg,4863
-biolmai/biolmai.py,sha256=CjaV-T1n5Kle8prUSEsIvSYcAA5CJ2XDU2mWsJYDhz8,5336
-biolmai/cli.py,sha256=rpet-mToHlSRIqRgSXGUbqjgPEk-c0nU_ZIalJ3dtjw,1936
-biolmai/cls.py,sha256=Hh_ggmCfDZGPSzYfCfXcFhvoOJVgpuc1rgwHdr7KGFY,29
-biolmai/const.py,sha256=CyZve7qZ8cnX9T4NvNxw2Xpi8QKPX7B_lfXxt8se1tc,1099
-biolmai/ltc.py,sha256=al7HZc5tLyUR5fmpIb95hOz5ctudVsc0xzjd_c2Ew3M,49
-biolmai/payloads.py,sha256=Si0EHKVNYGOAMAsiC4hEez8YZve88cYPu2KwBfaIN18,289
-biolmai/validate.py,sha256=lU-qT11xgB83q76-knKNygDMLAqRdLlmP9mLh6wqNNw,3130
-biolmai-0.1.4.dist-info/AUTHORS.rst,sha256=TB_ACuFPgVmxn1NspYwksTdT6jdZeShcxfafmi-XWKQ,158
-biolmai-0.1.4.dist-info/LICENSE,sha256=8yt0SdP38I7a3g0zWqZjNe0VSDQhJA4bWLQSqqKtAVg,583
-biolmai-0.1.4.dist-info/METADATA,sha256=xX62sswY4h8rheJlCZCmD_fmVmiKf1yAqdwZ5qU_g0c,1929
-biolmai-0.1.4.dist-info/WHEEL,sha256=a-zpFRIJzOq5QfuhBzbhiA1eHTzNCJn8OdRvhdNX0Rk,110
-biolmai-0.1.4.dist-info/entry_points.txt,sha256=ylQnDpCYrxF1F9z_T7NRQcYMWYF5ia_KsTUuboxjEAM,44
-biolmai-0.1.4.dist-info/top_level.txt,sha256=jyQO45JN3g_jbdI8WqMnb0aEIzf4h1MrmPAZkKgfnwY,8
-biolmai-0.1.4.dist-info/RECORD,,