prisma-api 0.4.3__tar.gz → 0.4.5__tar.gz

{prisma_api-0.4.3 → prisma_api-0.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: prisma_api
-Version: 0.4.3
+Version: 0.4.5
 Summary: A package for interacting with PrISMa Platform APIs. PrISMa is a holistic system for numerical synthesis and assessment of Metal-Organic Frameworks and their applications, for Direct Air Capture of CO2. For more information, see: https://prisma.hw.ac.uk.
 Author-email: RCCS-CaptureTeam <team@prisma-platform.org>
 License: GNUv3
@@ -165,7 +165,7 @@ The main client exposes these v1 methods:
 - `get_materials_data(payload={}, separate_experimental=True)`
 - `update_adsorption_singlepoint(df)`
 - `update_heat_capacity_all_tidy(df)`
-- `update_isotherm_h2(df)`
+- `update_isotherm_h2(df)` — deprecated; still works (the server stores its rows in `adsorption_isotherm`)
 - `update_mofchecker(df)`
 - `update_zeopp_metrics(df)`
 
@@ -181,6 +181,7 @@ Module-level helpers exported from the package:
 - `prisma_api.update_dev_mode`
 - `prisma_api.update_dev_host_port`
 - `prisma_api.locate_config`
+- `prisma_api.PrismaUpsertError`, `prisma_api.PrismaRowErrorWarning`, `prisma_api.PrismaUnknownFieldsWarning`, `prisma_api.PrismaNewStructureWarning`
 
 ## v2 wrapper list
 
@@ -266,6 +267,28 @@ All methods below are available on `api.v2`.
 - `get_carbon_zeopp_experimental(mof=None, limit=500, offset=0)`
 - `get_carbon_zeopp_experimental_item(item_id)`
 
+### AutoPrism tables
+
+- `get_computation_runs(workflow_id=None, step=None, status=None, limit=500, offset=0)` / `get_computation_run(run_id)`
+- `upsert_computation_runs(payload, timeout=None, raise_on_error=False)`
+- `get_adsorption_singlepoint(...)` / `get_adsorption_singlepoint_item(row_id)` / `upsert_adsorption_singlepoint(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)`
+- `get_heat_capacity(...)` / `get_heat_capacity_item(row_id)` / `upsert_heat_capacity(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)`
+- `get_isotherm_h2(...)` / `get_isotherm_h2_item(row_id)` / `upsert_isotherm_h2(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)` — deprecated; use the `adsorption_isotherm` methods with `component='H2'`
+- `get_adsorption_isotherm(structure=None, isotherm_id=None, component=None, temperature_K=None, pressure_bar=None, limit=500, offset=0, md5=None, match=None)` / `get_adsorption_isotherm_item(row_id)` / `upsert_adsorption_isotherm(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)` — every gas, H2 included; needs prisma_cloud **>= 0.6.16** (older servers return 404)
+- `get_mofchecker(...)` / `get_mofchecker_item(row_id)` / `upsert_mofchecker(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)`
+- `get_zeopp_metrics(...)` / `get_zeopp_metrics_item(row_id)` / `upsert_zeopp_metrics(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)`
+- `upsert_autoprism_cifs(cifs, tags=None, create_materials=True, batch_size=50, raise_on_error=False, timeout=300)` — AutoPrism's own CIFs, stored as `{structure}__autoprism_{md5[:12]}.cif`
+- `get_autoprism_collection(...)` / `upsert_autoprism_collection(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True, cif_tags=None)`
+
+The getters take `match="exact"` for an exact (case-insensitive) name match
+instead of the default substring match.
+
+Rejected rows (HTTP 207, or 400 when nothing is stored) raise
+`PrismaUpsertError` with `raise_on_error=True`, else emit
+`PrismaRowErrorWarning`. Ignored payload fields and newly created MOF records
+emit `PrismaUnknownFieldsWarning` / `PrismaNewStructureWarning`. See
+[API_REFERENCE_V2.md](API_REFERENCE_V2.md#autoprism-tables).
+
 ### TEA, LCA, cases, and scenarios
 
 - `get_output_kpis(scenario_id=None, mof=None, good_structure=None, limit=500, offset=0)`
@@ -373,7 +396,8 @@ pytest tests/ -v --cov=prisma_api --cov-report=term-missing
 
 ## Additional documentation
 
-- [API_REFERENCE.md](API_REFERENCE.md)
+- [API_REFERENCE_V1.md](API_REFERENCE_V1.md)
+- [API_REFERENCE_V2.md](API_REFERENCE_V2.md)
 - [DEVELOPMENT_SUMMARY.md](DEVELOPMENT_SUMMARY.md)
 - [User Guide.md](User%20Guide.md)
 
@@ -381,4 +405,6 @@ pytest tests/ -v --cov=prisma_api --cov-report=term-missing
 
 - Production v2 base URL: `https://prisma-platform.org/api/v2`
 - Authentication header: `X-API-Key`
-- Local development routing is controlled through config and `api.update_dev_mode(True)`
+- Local development routing is selected with `prisma_api.init(local_dev=True)`; the default targets production
+- 0.4.4: the `adsorption-isotherm` endpoints and the 400/notice handling need prisma_cloud >= 0.6.16
+- 0.4.5: H2 isotherms go through `upsert_adsorption_isotherm` (prisma_cloud >= 0.6.16); the H2-only methods and the `isotherm_H2s` collection key are deprecated. New `upsert_autoprism_cifs` uses the existing bundle upsert endpoint. AutoPrism getters take `match="exact"`.

{prisma_api-0.4.3 → prisma_api-0.4.5}/README.md

@@ -145,7 +145,7 @@ The main client exposes these v1 methods:
 - `get_materials_data(payload={}, separate_experimental=True)`
 - `update_adsorption_singlepoint(df)`
 - `update_heat_capacity_all_tidy(df)`
-- `update_isotherm_h2(df)`
+- `update_isotherm_h2(df)` — deprecated; still works (the server stores its rows in `adsorption_isotherm`)
 - `update_mofchecker(df)`
 - `update_zeopp_metrics(df)`
 
@@ -161,6 +161,7 @@ Module-level helpers exported from the package:
 - `prisma_api.update_dev_mode`
 - `prisma_api.update_dev_host_port`
 - `prisma_api.locate_config`
+- `prisma_api.PrismaUpsertError`, `prisma_api.PrismaRowErrorWarning`, `prisma_api.PrismaUnknownFieldsWarning`, `prisma_api.PrismaNewStructureWarning`
 
 ## v2 wrapper list
 
@@ -246,6 +247,28 @@ All methods below are available on `api.v2`.
 - `get_carbon_zeopp_experimental(mof=None, limit=500, offset=0)`
 - `get_carbon_zeopp_experimental_item(item_id)`
 
+### AutoPrism tables
+
+- `get_computation_runs(workflow_id=None, step=None, status=None, limit=500, offset=0)` / `get_computation_run(run_id)`
+- `upsert_computation_runs(payload, timeout=None, raise_on_error=False)`
+- `get_adsorption_singlepoint(...)` / `get_adsorption_singlepoint_item(row_id)` / `upsert_adsorption_singlepoint(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)`
+- `get_heat_capacity(...)` / `get_heat_capacity_item(row_id)` / `upsert_heat_capacity(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)`
+- `get_isotherm_h2(...)` / `get_isotherm_h2_item(row_id)` / `upsert_isotherm_h2(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)` — deprecated; use the `adsorption_isotherm` methods with `component='H2'`
+- `get_adsorption_isotherm(structure=None, isotherm_id=None, component=None, temperature_K=None, pressure_bar=None, limit=500, offset=0, md5=None, match=None)` / `get_adsorption_isotherm_item(row_id)` / `upsert_adsorption_isotherm(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)` — every gas, H2 included; needs prisma_cloud **>= 0.6.16** (older servers return 404)
+- `get_mofchecker(...)` / `get_mofchecker_item(row_id)` / `upsert_mofchecker(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)`
+- `get_zeopp_metrics(...)` / `get_zeopp_metrics_item(row_id)` / `upsert_zeopp_metrics(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True)`
+- `upsert_autoprism_cifs(cifs, tags=None, create_materials=True, batch_size=50, raise_on_error=False, timeout=300)` — AutoPrism's own CIFs, stored as `{structure}__autoprism_{md5[:12]}.cif`
+- `get_autoprism_collection(...)` / `upsert_autoprism_collection(payload, meta_provenance=None, repo_dir=None, timeout=None, raise_on_error=False, check_ids=True, cif_tags=None)`
+
+The getters take `match="exact"` for an exact (case-insensitive) name match
+instead of the default substring match.
+
+Rejected rows (HTTP 207, or 400 when nothing is stored) raise
+`PrismaUpsertError` with `raise_on_error=True`, else emit
+`PrismaRowErrorWarning`. Ignored payload fields and newly created MOF records
+emit `PrismaUnknownFieldsWarning` / `PrismaNewStructureWarning`. See
+[API_REFERENCE_V2.md](API_REFERENCE_V2.md#autoprism-tables).
+
 ### TEA, LCA, cases, and scenarios
 
 - `get_output_kpis(scenario_id=None, mof=None, good_structure=None, limit=500, offset=0)`
@@ -353,7 +376,8 @@ pytest tests/ -v --cov=prisma_api --cov-report=term-missing
 
 ## Additional documentation
 
-- [API_REFERENCE.md](API_REFERENCE.md)
+- [API_REFERENCE_V1.md](API_REFERENCE_V1.md)
+- [API_REFERENCE_V2.md](API_REFERENCE_V2.md)
 - [DEVELOPMENT_SUMMARY.md](DEVELOPMENT_SUMMARY.md)
 - [User Guide.md](User%20Guide.md)
 
@@ -361,4 +385,6 @@ pytest tests/ -v --cov=prisma_api --cov-report=term-missing
 
 - Production v2 base URL: `https://prisma-platform.org/api/v2`
 - Authentication header: `X-API-Key`
-- Local development routing is controlled through config and `api.update_dev_mode(True)`
+- Local development routing is selected with `prisma_api.init(local_dev=True)`; the default targets production
+- 0.4.4: the `adsorption-isotherm` endpoints and the 400/notice handling need prisma_cloud >= 0.6.16
+- 0.4.5: H2 isotherms go through `upsert_adsorption_isotherm` (prisma_cloud >= 0.6.16); the H2-only methods and the `isotherm_H2s` collection key are deprecated. New `upsert_autoprism_cifs` uses the existing bundle upsert endpoint. AutoPrism getters take `match="exact"`.

prisma_api-0.4.5/prisma_api/__init__.py

@@ -0,0 +1,31 @@
+from importlib.metadata import PackageNotFoundError
+from importlib.metadata import version as _version
+
+try:
+    __version__ = _version("prisma_api")
+except PackageNotFoundError:  # running from a source tree without installing
+    __version__ = "0+unknown"
+
+
+from prisma_api.config import locate_config, update_dev_host_port, update_dev_mode
+from prisma_api.prisma_api import prisma_api as init  # main client
+from prisma_api.prisma_api_v2 import (  # v2 client (also api.v2) and upsert failure signals
+    PrismaAPIv2,
+    PrismaNewStructureWarning,
+    PrismaRowErrorWarning,
+    PrismaUnknownFieldsWarning,
+    PrismaUpsertError,
+)
+
+__all__ = [
+    "PrismaAPIv2",
+    "PrismaNewStructureWarning",
+    "PrismaRowErrorWarning",
+    "PrismaUnknownFieldsWarning",
+    "PrismaUpsertError",
+    "__version__",
+    "init",
+    "locate_config",
+    "update_dev_host_port",
+    "update_dev_mode",
+]

{prisma_api-0.4.3 → prisma_api-0.4.5}/prisma_api/config.py

@@ -1,11 +1,10 @@
 import os
 import sys
 from pathlib import Path
+
 import pandas as pd
-import yaml
 import platformdirs
-
-
+import yaml
 
 ### Helper functions for config management
 
@@ -42,7 +41,7 @@ def load_config():
     return cfg
 
 # Internal function to create config.yaml
-def create_config_file(api_key: str = None):
+def create_config_file(api_key: str | None = None):
     """
     Create config.yaml. If api_key is None, prompt via CLI.
 

{prisma_api-0.4.3 → prisma_api-0.4.5}/prisma_api/prisma_api.py

@@ -1,14 +1,15 @@
+import math
 import os
 import warnings
-from .config import get_or_create_config, update_dev_mode as _update_dev_mode
-from .prisma_api_v2 import PrismaAPIv2
-from pathlib import Path
+
+import numpy as np
 import pandas as pd
 import requests
 
-import numpy as np
-import json
-import math
+from .config import get_or_create_config
+from .config import update_dev_mode as _update_dev_mode
+from .prisma_api_v2 import PrismaAPIv2
+
 
 def _safe_nan_check(x):
     if x is None:
@@ -23,7 +24,7 @@ def _safe_nan_check(x):
   
 
 # prisma_api main class
-class prisma_api():
+class prisma_api:
 
     def __init__(self, use_config_file=True, local_dev: bool = False,
                  upload_timeout: int = 120):
@@ -91,7 +92,7 @@ class prisma_api():
         )
         return _update_dev_mode(dev)
         
-    def get_mofs(self, payload={}):
+    def get_mofs(self, payload: dict | None = None):
 
         api = self
 
@@ -105,7 +106,7 @@ class prisma_api():
             "Content-Type": "application/json"
         }
 
-        response = requests.post(url, json=payload, headers=headers, timeout=60)
+        response = requests.post(url, json=payload or {}, headers=headers, timeout=60)
         data = response.json()['data']
 
         data = pd.DataFrame.from_dict(data)
@@ -113,7 +114,7 @@ class prisma_api():
         return data
     
     
-    def get_carbon_isotherms(self, payload={}):
+    def get_carbon_isotherms(self, payload: dict | None = None):
 
         api = self
 
@@ -128,7 +129,7 @@ class prisma_api():
         }
 
         try:
-            response = requests.post(url, json=payload, headers=headers, timeout=60)
+            response = requests.post(url, json=payload or {}, headers=headers, timeout=60)
             data = response.json()['data']
 
             data = pd.DataFrame.from_dict(data)
@@ -147,11 +148,11 @@ class prisma_api():
 
             return data
         
-        except Exception as e:
+        except Exception:  # noqa: BLE001 - v1 contract: print and return empty
             print("Error retrieving carbon isotherms: check that the query parameter names are correct.")
             return pd.DataFrame()
     
-    def get_carbon_data_nested(self, payload={}, safe_names=False):
+    def get_carbon_data_nested(self, payload: dict | None = None, safe_names=False):
         """
         Get carbon data with nested structure, returned as separate DataFrames.
 
@@ -180,7 +181,7 @@ class prisma_api():
         }
 
         try:
-            response = requests.post(url, json=payload, headers=headers, timeout=60)
+            response = requests.post(url, json=payload or {}, headers=headers, timeout=60)
             data = response.json()
 
             col_names_carbon = data.get('meta', {}).get('original_column_names', {})
@@ -234,11 +235,11 @@ class prisma_api():
                 }
             }
 
-        except Exception as e:
+        except Exception as e:  # noqa: BLE001 - v1 contract: print and return empty
             print(f"Error retrieving carbon data nested: {e}")
             return {}
     
-    def get_materials_data(self, payload={}, separate_experimental=True):
+    def get_materials_data(self, payload: dict | None = None, separate_experimental=True):
         """
         Args:
             payload:                 Dictionary containing query parameters for filtering.
@@ -279,12 +280,12 @@ class prisma_api():
             source_key = None
             for name, endpoint in urls.items():
                 try:
-                    response = requests.post(endpoint, json=payload, headers=headers, timeout=60)
+                    response = requests.post(endpoint, json=payload or {}, headers=headers, timeout=60)
                     data_raw = response.json()
                     if data_raw.get('data'):
                         source_key = name
                         break
-                except Exception:
+                except Exception:  # noqa: BLE001, S112 - endpoint fallback: try the next one
                     continue
             
             if data_raw is None:
@@ -406,7 +407,7 @@ class prisma_api():
                     'meta': {'source': source_key},
                 }
 
-        except Exception as e:
+        except Exception as e:  # noqa: BLE001 - v1 contract: print and return empty
             print(f"Error retrieving materials data: {e}")
             return {}
     
@@ -446,8 +447,6 @@ class prisma_api():
         if df.empty:
             return "[]"
         
-        import numpy as np
-        import json
         
         # Use pandas to_json which handles NaN properly, then parse back
         df_clean = df.copy()