v1.0.0-rc.179 (#90)

* Rugnux: Stills processing needs only the unit cell and space group beyond what the file records - detector distance, beam centre, tilt, panel placement, saturation level, gain and polarisation plane are found from the images - and is up to twice as fast.
* Rugnux: Stills can be indexed without a GPU, with a CPU implementation of the fast-feedback indexer (macOS, computers without a GPU).
* Rugnux: Rotation and stills data are integrated in the detector's own units with one gain model, improving data from CCD detectors.
* Web frontend: The Rugnux live page shows the placed model with its electron density and anomalous difference map in a Mol* viewer.

Reviewed-on: #90
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

docs/python_client/README.md

@@ -22,8 +22,8 @@ communicate through network calls or other mechanisms.
 
 This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
-- API version: 1.0.0-rc.178
-- Package version: 1.0.0-rc.178
+- API version: 1.0.0-rc.179
+- Package version: 1.0.0-rc.179
 - Generator version: 7.20.0
 - Build package: org.openapitools.codegen.languages.PythonClientCodegen
 
@@ -159,6 +159,8 @@ Class | Method | HTTP request | Description
 *DefaultApi* | [**preview_plot_bin_get**](docs/DefaultApi.md#preview_plot_bin_get) | **GET** /preview/plot.bin | Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. 
 *DefaultApi* | [**preview_plot_get**](docs/DefaultApi.md#preview_plot_get) | **GET** /preview/plot | Generate 1D plot from Jungfraujoch
 *DefaultApi* | [**result_scan_get**](docs/DefaultApi.md#result_scan_get) | **GET** /result/scan | Get full scan result
+*DefaultApi* | [**rugnux_map_ccp4_get**](docs/DefaultApi.md#rugnux_map_ccp4_get) | **GET** /rugnux/map.ccp4 | Get an electron-density map of the last rugnux live run
+*DefaultApi* | [**rugnux_model_cif_get**](docs/DefaultApi.md#rugnux_model_cif_get) | **GET** /rugnux/model.cif | Get the model as placed by the last rugnux live run
 *DefaultApi* | [**rugnux_status_get**](docs/DefaultApi.md#rugnux_status_get) | **GET** /rugnux/status | Get live rugnux processing status of the last collection
 *DefaultApi* | [**start_post**](docs/DefaultApi.md#start_post) | **POST** /start | Start detector
 *DefaultApi* | [**statistics_calibration_get**](docs/DefaultApi.md#statistics_calibration_get) | **GET** /statistics/calibration | Get calibration statistics

docs/python_client/docs/DefaultApi.md

@@ -62,6 +62,8 @@ Method | HTTP request | Description
 [**preview_plot_bin_get**](DefaultApi.md#preview_plot_bin_get) | **GET** /preview/plot.bin | Generate 1D plot from Jungfraujoch and send in raw binary format. Data are provided as (32-bit) float binary array. This format doesn't transmit information about X-axis, only values, so it is of limited use for azimuthal integration. 
 [**preview_plot_get**](DefaultApi.md#preview_plot_get) | **GET** /preview/plot | Generate 1D plot from Jungfraujoch
 [**result_scan_get**](DefaultApi.md#result_scan_get) | **GET** /result/scan | Get full scan result
+[**rugnux_map_ccp4_get**](DefaultApi.md#rugnux_map_ccp4_get) | **GET** /rugnux/map.ccp4 | Get an electron-density map of the last rugnux live run
+[**rugnux_model_cif_get**](DefaultApi.md#rugnux_model_cif_get) | **GET** /rugnux/model.cif | Get the model as placed by the last rugnux live run
 [**rugnux_status_get**](DefaultApi.md#rugnux_status_get) | **GET** /rugnux/status | Get live rugnux processing status of the last collection
 [**start_post**](DefaultApi.md#start_post) | **POST** /start | Start detector
 [**statistics_calibration_get**](DefaultApi.md#statistics_calibration_get) | **GET** /statistics/calibration | Get calibration statistics
@@ -4073,6 +4075,168 @@ This endpoint does not need any parameter.
 
 [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
 
+# **rugnux_map_ccp4_get**
+> bytearray rugnux_map_ccp4_get(type=type)
+
+Get an electron-density map of the last rugnux live run
+
+The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map
+coefficients written to `_maps.mtz` (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where
+the model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and
+RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones.
+
+
+### Example
+
+* Bearer Authentication (bearerAuth):
+
+```python
+import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+# The client must configure the authentication and authorization parameters
+# in accordance with the API server security policy.
+# Examples for each auth method are provided below, use the example that
+# satisfies your auth use case.
+
+# Configure Bearer authorization: bearerAuth
+configuration = jfjoch_client.Configuration(
+    access_token = os.environ["BEARER_TOKEN"]
+)
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+    type = 2fofc # str | `2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map; `anom`: the anomalous difference map, (F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (`anomalous_map` in `/rugnux/status`)  (optional) (default to 2fofc)
+
+    try:
+        # Get an electron-density map of the last rugnux live run
+        api_response = api_instance.rugnux_map_ccp4_get(type=type)
+        print("The response of DefaultApi->rugnux_map_ccp4_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->rugnux_map_ccp4_get: %s\n" % e)
+```
+
+
+
+### Parameters
+
+
+Name | Type | Description  | Notes
+------------- | ------------- | ------------- | -------------
+ **type** | **str**| `2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map; `anom`: the anomalous difference map, (F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (`anomalous_map` in `/rugnux/status`)  | [optional] [default to 2fofc]
+
+### Return type
+
+**bytearray**
+
+### Authorization
+
+[bearerAuth](../README.md#bearerAuth)
+
+### HTTP request headers
+
+ - **Content-Type**: Not defined
+ - **Accept**: application/octet-stream, text/plain
+
+### HTTP response details
+
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | Map |  -  |
+**400** | Unknown map type |  -  |
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
+**404** | The last rugnux live run placed no model or made no maps, or (`anom`) has no Bijvoet pairs |  -  |
+
+[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
+
+# **rugnux_model_cif_get**
+> bytearray rugnux_model_cif_get()
+
+Get the model as placed by the last rugnux live run
+
+The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
+`_model.cif` file written beside the data: the data's cell and space group, with the input model's own
+metadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.
+
+
+### Example
+
+* Bearer Authentication (bearerAuth):
+
+```python
+import jfjoch_client
+from jfjoch_client.rest import ApiException
+from pprint import pprint
+
+# Defining the host is optional and defaults to http://localhost:5232
+# See configuration.py for a list of all supported configuration parameters.
+configuration = jfjoch_client.Configuration(
+    host = "http://localhost:5232"
+)
+
+# The client must configure the authentication and authorization parameters
+# in accordance with the API server security policy.
+# Examples for each auth method are provided below, use the example that
+# satisfies your auth use case.
+
+# Configure Bearer authorization: bearerAuth
+configuration = jfjoch_client.Configuration(
+    access_token = os.environ["BEARER_TOKEN"]
+)
+
+# Enter a context with an instance of the API client
+with jfjoch_client.ApiClient(configuration) as api_client:
+    # Create an instance of the API class
+    api_instance = jfjoch_client.DefaultApi(api_client)
+
+    try:
+        # Get the model as placed by the last rugnux live run
+        api_response = api_instance.rugnux_model_cif_get()
+        print("The response of DefaultApi->rugnux_model_cif_get:\n")
+        pprint(api_response)
+    except Exception as e:
+        print("Exception when calling DefaultApi->rugnux_model_cif_get: %s\n" % e)
+```
+
+
+
+### Parameters
+
+This endpoint does not need any parameter.
+
+### Return type
+
+**bytearray**
+
+### Authorization
+
+[bearerAuth](../README.md#bearerAuth)
+
+### HTTP request headers
+
+ - **Content-Type**: Not defined
+ - **Accept**: chemical/x-mmcif, text/plain
+
+### HTTP response details
+
+| Status code | Description | Response headers |
+|-------------|-------------|------------------|
+**200** | Placed model |  -  |
+**401** | The current dataset is protected and no valid bearer token was presented. |  -  |
+**404** | The last rugnux live run placed no model |  -  |
+
+[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
+
 # **rugnux_status_get**
 > RugnuxLiveStatus rugnux_status_get()
 

docs/python_client/docs/RugnuxLiveStatus.md

@@ -7,6 +7,8 @@ Live rugnux processing of the last collection; kept until the next collection st
 Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------
 **state** | **str** |  | 
+**placed_model** | **bool** | The run placed the model: it can be fetched from `/rugnux/model.cif` and its maps from `/rugnux/map.ccp4`.  | 
+**anomalous_map** | **bool** | The merge kept the Bijvoet pairs, so with the placed model there is an anomalous difference map (`/rugnux/map.ccp4?type=anom`).  | 
 **probe** | **str** | Answer of the early lattice probe on the first 60 degrees; empty until it answers | 
 **probe_s** | **float** | When the probe answered, since the first image | [optional] 
 **start_to_first_image_s** | **float** | From the START message to the first image; set once the first image arrives | [optional]