Version 5.1.4 bump

dev-requirements.txt

@@ -1,4 +1,3 @@
 grpcio-tools
-minknow-api-service-plugin
 pre-commit
 pytest

proto/minknow_api/analysis_configuration.proto

@@ -460,25 +460,12 @@ message ChannelStates {
 message GetAnalysisConfigurationRequest {
 }
 
-
-// Since 5.3
-message ScalingParams
-{
-    // If present, must be 20 long
-    repeated float q_weights_shift = 1;
-
-    // If present, must be 20 long
-    repeated float q_weights_scale = 2;   
-}
-
 message AnalysisConfiguration {
     EventDetection event_detection = 1;
     ReadDetectionParams read_detection = 2;
 
     ReadClassificationParams read_classification = 4;
     map<string, ChannelStates> channel_states = 7;
-
-    ScalingParams scaling = 8;
 }
 
 message SetAnalysisConfigurationResponse {
@@ -975,34 +962,6 @@ message WriterConfiguration {
 
         // How many files are placed in each batch (after batch_count files {batch_number} is increased in the filename).
         uint32 batch_count = 3;
-
-        // If true minknow will only write the primary alignment for each read.
-        bool disable_writing_multiple_alignments = 4;
-    }
-
-    message ReadPod5Configuration {
-        // Control if a POD5 file should be generated per channel.
-        ChannelConfiguration enable = 1;
-
-        // The pattern used to find a POD5 files name.
-        //
-        // default: pod5{basecall_status}/{flow_cell_id}_{run_id}_{batch_number}.pod5
-        // Where each {xxx} section is replaced with an attribute from the minknow state when the file is written.
-        //
-        // See file pattern attributes above.
-        string file_pattern = 2;
-
-        // How many files are placed in each batch (after batch_count files {batch_number} is increased in the filename).
-        //
-        // Set to zero to disable batching.
-        uint32 batch_count = 3;
-
-        // Prevent reads which have successfully basecalled being written to pod5.
-        bool disable_writing_passed_reads = 4;
-        // Prevent reads which have failed basecalling being written to pod5.
-        bool disable_writing_failed_reads = 5;
-        // disable writing reads which have been force skipped by the basecaller.
-        bool disable_writing_force_skipped_reads = 6;
     }
 
     message ReadProtobufConfiguration {
@@ -1098,9 +1057,6 @@ message WriterConfiguration {
 
     // Control settings for the report writer
     message ReportConfiguration {
-        // DEPRECATED 6.0: As of 5.1 a pdf report is not generated at all. This field will
-        // be removed in 6.0
-        //
         // The pattern used to find the pdf report filename. If left empty but output is
         // enabled a default pattern is used.
         //
@@ -1219,11 +1175,6 @@ message WriterConfiguration {
     // If not specified, no BAM outputs are generated.
     ReadBamConfiguration read_bam = 8;
 
-    // Configuration for the POD5 writer.
-    //
-    // If not specified no POD5 outputs are generated.
-    ReadPod5Configuration read_pod5 = 10;
-
     // Configuration for the protobuf writer.
     //
     // If not specified, no protobuf outputs are generated.

proto/minknow_api/basecaller.proto

@@ -261,9 +261,6 @@ message StartPostProcessingProtocolRequest {
     string input_fast5_directory = 2;
     string input_fastq_directory = 3;
     string input_bam_directory = 4;
-
-    // Path to the sample sheet output by minknow
-    string sample_sheet_path = 8;
 
     // Output directory where the analysed output should be written.
     string output_directory = 5;

proto/minknow_api/device.proto

@@ -352,7 +352,6 @@ message GetDeviceInfoResponse {
         PROMETHION = 3;
         MINION_MK1C = 4;
         TRAXION = 5;
-        P2_SOLO = 6;
     }
 
     // A unique identifier for the device.

proto/minknow_api/instance.proto

@@ -295,13 +295,13 @@ message DeviceInfo {
 }
 
 message BasecallSpeed {
-    // Mean basecall speed, in bases per second.
-    //
-    // This value is only streamed for acquisitions where basecalling is enabled.
-    //
-    // The value reported here is the value stored in last completed basecall boxplot bucket
-    // Each boxplot bucket covers a duration of `boxplot_time_coverage_in_minutes`
-    float mean_basecall_speed = 1;
+        // Mean basecall speed, in bases per second.
+        //
+        // This value is only streamed for acquisitions where basecalling is enabled.
+        //
+        // The value reported here is the value stored in last completed basecall boxplot bucket
+        // Each boxplot bucket covers a duration of `boxplot_time_coverage_in_minutes`
+        float mean_basecall_speed = 1;
 }
 
 message N50 {

proto/minknow_api/manager.proto

@@ -556,30 +556,6 @@ message FlowCellPosition {
     //
     // Since 5.0.
     SimpleProtocolState protocol_state = 9;
-
-    // Whether the device is simulated.
-    //
-    // If this is true, there is no physical device - MinKNOW is simulating it. If it is false,
-    // MinKNOW will be acquiring data from a real device.
-    //
-    // Since 5.2
-    bool is_simulated = 10;
-
-    // The type of the device.
-    //
-    // Since 5.2
-    minknow_api.device.GetDeviceInfoResponse.DeviceType device_type = 11;
-
-    // The name of the device this flow cell position is part of.
-    //
-    // For an integrated position, this will be the host serial, as returned by describe_host().
-    //
-    // For a MinION Mk1B, this will be the same as the `name` field.
-    //
-    // For a P2 Solo, this will be the name of the P2 Solo unit.
-    //
-    // Since 5.3
-    string parent_name = 12;
 }
 
 message FlowCellPositionsRequest {

proto/minknow_api/report_data.proto

@@ -10,11 +10,13 @@ import "minknow_api/statistics.proto";
 
 enum AcquisitionOutputTypes {
     AllData = 0;
+
     SplitByBarcodeAndAlignment = 1;
+
     SplitByBarcode = 2;
     SplitByAlignment = 3;
+
     SplitByEndReason = 4;
-    SplitByBedRegion = 5;
 }
 
 message AcquisitionOutput {

proto/minknow_api/statistics.proto

@@ -441,11 +441,6 @@ message AcquisitionOutputKey {
     // If unspecified all alignment regions are returned.
     string alignment_bed_file_region = 3;
 
-    // An alias to `alignment_bed_file_region`
-    //
-    // An optional name can be used to identify a target region in the bed file
-    string alignment_bed_file_region_name = 8;
-
     // Only return data for the given lamp barcode.
     //
     // Special values:

python/minknow_api/__init__.py

@@ -86,20 +86,6 @@
 
 from minknow_api.manager import get_local_authentication_token_file
 
-# Try and import from minknow_api_production package
-try:
-    from minknow_api_production import (
-        production_service,
-        production_pb2,
-        production_pb2_grpc,
-    )
-
-    sys.modules["minknow_api.production_service"] = production_service
-    sys.modules["minknow_api.production_pb2"] = production_pb2
-    sys.modules["minknow_api.production_pb2_grpc"] = production_pb2_grpc
-except ImportError:
-    pass
-
 #
 # Services
 #

python/minknow_api/_version.py

@@ -1 +1 @@
-__version__ = '5.1.3'
+__version__ = '5.1.4'

python/minknow_api/analysis_configuration_service.py

@@ -16,7 +16,6 @@
     "ReadClassificationParams",
     "ChannelStates",
     "GetAnalysisConfigurationRequest",
-    "ScalingParams",
     "AnalysisConfiguration",
     "SetAnalysisConfigurationResponse",
     "ResetAnalysisConfigurationRequest",
@@ -155,7 +154,6 @@ def set_analysis_configuration(self, _message=None, _timeout=None, **kwargs):
             read_detection (minknow_api.analysis_configuration_pb2.ReadDetectionParams, optional): 
             read_classification (minknow_api.analysis_configuration_pb2.ReadClassificationParams, optional): 
             channel_states (minknow_api.analysis_configuration_pb2.AnalysisConfiguration.ChannelStatesEntry, optional): 
-            scaling (minknow_api.analysis_configuration_pb2.ScalingParams, optional): 
 
         Returns:
             minknow_api.analysis_configuration_pb2.SetAnalysisConfigurationResponse
@@ -192,10 +190,6 @@ def set_analysis_configuration(self, _message=None, _timeout=None, **kwargs):
             for key, value in kwargs['channel_states'].items():
                 _message.channel_states[key].CopyFrom(value)
 
-        if "scaling" in kwargs:
-            unused_args.remove("scaling")
-            _message.scaling.CopyFrom(kwargs['scaling'])
-
         if len(unused_args) > 0:
             raise ArgumentError("Unexpected keyword arguments to set_analysis_configuration: '{}'".format(", ".join(unused_args)))
 
@@ -793,9 +787,6 @@ def set_writer_configuration(self, _message=None, _timeout=None, **kwargs):
             read_bam (minknow_api.analysis_configuration_pb2.WriterConfiguration.ReadBamConfiguration, optional): Configuration for the BAM writer.
 
                 If not specified, no BAM outputs are generated.
-            read_pod5 (minknow_api.analysis_configuration_pb2.WriterConfiguration.ReadPod5Configuration, optional): Configuration for the POD5 writer.
-
-                If not specified no POD5 outputs are generated.
             read_protobuf (minknow_api.analysis_configuration_pb2.WriterConfiguration.ReadProtobufConfiguration, optional): Configuration for the protobuf writer.
 
                 If not specified, no protobuf outputs are generated.
@@ -843,10 +834,6 @@ def set_writer_configuration(self, _message=None, _timeout=None, **kwargs):
             unused_args.remove("read_bam")
             _message.read_bam.CopyFrom(kwargs['read_bam'])
 
-        if "read_pod5" in kwargs:
-            unused_args.remove("read_pod5")
-            _message.read_pod5.CopyFrom(kwargs['read_pod5'])
-
         if "read_protobuf" in kwargs:
             unused_args.remove("read_protobuf")
             _message.read_protobuf.CopyFrom(kwargs['read_protobuf'])

python/minknow_api/basecaller_service.py

@@ -324,7 +324,6 @@ def start_post_processing_protocol(self, _message=None, _timeout=None, **kwargs)
             input_fast5_directory (str, optional): Input directories for the protocol (omit those which the protocol doesn't require).
             input_fastq_directory (str, optional): 
             input_bam_directory (str, optional): 
-            sample_sheet_path (str, optional): Path to the sample sheet output by minknow
             output_directory (str, optional): Output directory where the analysed output should be written.
             setting_values (minknow_api.basecaller_pb2.StartPostProcessingProtocolRequest.SettingValuesEntry, optional): Configured values for display settings for the protocol (see basecaller.list_settings_for_protocol)
                 keys missing from the original protocol will cause errors.
@@ -367,10 +366,6 @@ def start_post_processing_protocol(self, _message=None, _timeout=None, **kwargs)
             unused_args.remove("input_bam_directory")
             _message.input_bam_directory = kwargs['input_bam_directory']
 
-        if "sample_sheet_path" in kwargs:
-            unused_args.remove("sample_sheet_path")
-            _message.sample_sheet_path = kwargs['sample_sheet_path']
-
         if "output_directory" in kwargs:
             unused_args.remove("output_directory")
             _message.output_directory = kwargs['output_directory']