Version 6.2.1 bump

Author: minknowbot

.github/workflows/pypi-publish.yml

@@ -28,4 +28,4 @@ jobs:
           uses: pypa/gh-action-pypi-publish@master
           with:
             user: __token__
-            password: ${{ secrets.PYPI_API_TOKEN }}
+            password: ${{ secrets.PYPI_API_TOKEN }}

BREAKING_CHANGES_IN_5.0.md

@@ -4,7 +4,7 @@ The 5.0 release of MinKNOW API, describing the API for MinKNOW Core 5.0, has sev
 changes from earlier 4.x versions, and code using the API will need to be updated to suit.
 
 The breaking changes are documented below.  There also some changes to the API that do not
-break compatibility with older versions, such as the addition of new RPC's; these are not 
+break compatibility with older versions, such as the addition of new RPC's; these are not
 documented here.
 
 
@@ -18,43 +18,43 @@ No RPCs have been removed from the MinKNOW API since MinKNOW Core 4.0.
 Note that some messages have had their fields renumbered.  The wire format of these messages will
 not be compatible with earlier 4.x versions.
 
-Some messages have had fields renamed, but using the same number as in 4.x.  These messages will 
+Some messages have had fields renamed, but using the same number as in 4.x.  These messages will
 be wire compatible with 4.x, although the interpretation of these fields may have changed.  Code
 which uses these renamed fields will not be compatible.
 
 The following messages have had their fields changed:
 
 ### `analysis_configuration.proto`
 
-* `ReportConfiguration.ReportConfiguration`: The `markdown_report_file_pattern` field has been 
+* `ReportConfiguration.ReportConfiguration`: The `markdown_report_file_pattern` field has been
   renumbered to 8.  Field number 2 is now `json_report_file_pattern`
-  
+
 ### `instance.proto`
 
-* `GetVersionInfoResponse`: The `protocols` field has been renamed to `bream`, and the 
+* `GetVersionInfoResponse`: The `protocols` field has been renamed to `bream`, and the
   `configuration` field renamed to `protocol_configuration`, to more accurately reflect
   the contents of the packages these fields relate to.
- 
+
 ### `keystore.proto`
 
 * `StoreRequest`: When using the `lifetime` field to store a value in the manager, the only valid
   values are `UNTIL_INSTANCE_END` and `PERSIST_ACROSS_RESTARTS`.  Using any other value will cause
-  the call to fail with `INVALID_ARGUMENT` 
+  the call to fail with `INVALID_ARGUMENT`
 
 ### `manager.proto`
 
-* `FlowCellPosition.RpcPorts`: The fields `insecure` and `insecure_grpc_web` have been removed, 
+* `FlowCellPosition.RpcPorts`: The fields `insecure` and `insecure_grpc_web` have been removed,
   as it is no longer possible to use the gRPC protocols without TLS.
 
 ### `statistics.proto`
 
-* `AcquisitionOutputBucket` has been renamed to `AcquisitionOutputSnapshot`, as this message 
+* `AcquisitionOutputBucket` has been renamed to `AcquisitionOutputSnapshot`, as this message
   really reflects a snapshot of data at a given time point.  The field `bucket` has been renamed
-  to `seconds`, as it indicates the time point.  
+  to `seconds`, as it indicates the time point.
 * `StreamAcquisitionOutputResponse`: The submessage `FilteredBuckets` has been
   renamed to `FilteredSnapshots`.  The `buckets` field in both messages has been renamed
   to `snapshots`.
-* `WriterOutputBucket` has been renamed to `WriterOutputSnapshot`, as this message 
+* `WriterOutputBucket` has been renamed to `WriterOutputSnapshot`, as this message
   really reflects a snapshot of data at a given time point.  The field `bucket` has been renamed
-  to `seconds`, as it indicates the time point. 
+  to `seconds`, as it indicates the time point.
 * `StreamWriterOutputResponse`: The `buckets` field has been renamed to `snapshots`.

BUILD.md

@@ -1,10 +1,10 @@
 Building the python client
 ==========================
 
-The Python code has already been pre-generated from the .proto files, so to install it 
+The Python code has already been pre-generated from the .proto files, so to install it
 just run:
 
 ```bash
 cd python
 python -m pip install .
-```
+```

LICENSE.txt

@@ -360,4 +360,3 @@ You may add additional accurate notices of copyright ownership.
 
     This Source Code Form is "Incompatible With Secondary Licenses", as
     defined by the Mozilla Public License, v. 2.0.
-

README.md

@@ -18,7 +18,7 @@ including gathering information about running or finished experiments, starting
 experiments, and even exerting more fine-grained control. Anything that can be done via MinKNOW's
 user interface (and more) can be done using the APIs in this project.
 
-This project is targetted at LIMS developers or developers of other tools that have a need to
+This project is targeted at LIMS developers or developers of other tools that have a need to
 integrate with MinKNOW. Some familiarity with Python is expected (although the APIs can be used from
 other languages), as the examples are written in Python. If you are not familiar with [gRPC][grpc],
 it is worth reading through some of the [gRPC documentation][grpc-docs] to get a feel for it.

dev-requirements.txt

@@ -1,6 +1,6 @@
-cryptography~=39.0
-grpcio==1.60.0
-grpcio-tools==1.60.0
+cryptography~=42.0
+grpcio==1.60.1
+grpcio-tools==1.60.1
 minknow-api-service-plugin
 pre-commit
 pytest

proto/minknow_api/acquisition.proto

@@ -107,6 +107,13 @@ service AcquisitionService {
         option idempotency_level = IDEMPOTENT;
     }
 
+    // Find the signal reader in use. This may have been configured by MinKNOW prior to a protocol being begun.
+    //
+    // Since 6.2
+    rpc get_signal_reader (GetSignalReaderRequest) returns (GetSignalReaderResponse) {
+        option idempotency_level = IDEMPOTENT;
+    }
+
     // Set the bream information for the current acquisition.
     //
     // This should only be called by the protocol. It will only affect the last acquisition that was
@@ -401,6 +408,10 @@ enum AcquisitionState {
     // The acquisition period finished on its own and
     // did not report an error.
     ACQUISITION_COMPLETED = 3;
+
+    // The acquisition period is paused.
+    // that is, no data transfer occurring.
+    ACQUISITION_PAUSED = 4;
 }
 
 enum AcquisitionStopReason {
@@ -452,10 +463,10 @@ enum StartupState {
     // Setting up data writers for outputting reads/files.
     STARTUP_INITIALISING_DATA_WRITERS = 5;
 
-    // Initialsing storage for in flight reads.
+    // Initialising storage for in flight reads.
     STARTUP_INITIALISING_INTERMEDIATE_DATA_STORAGE = 6;
 
-    // Initialsing storage for run statistics.
+    // Initialising storage for run statistics.
     STARTUP_INITIALISING_STATISTICS = 7;
 }
 
@@ -530,7 +541,7 @@ message AcquisitionYieldSummary
     // As above, but counted in bases rather than basecalls.
     TotalsPerDuplexCategory basecalled_pass_bases_split = 24;
     TotalsPerDuplexCategory basecalled_fail_bases_split = 25;
-    
+
     // Number of raw samples which have been called.
     int64 basecalled_samples = 6;
 
@@ -709,7 +720,7 @@ message AcquisitionConfigSummary {
     bool fastq_reads_enabled = 5;
     // Determine if pod5 reads were enabled for the run.
     bool pod5_reads_enabled = 22;
-    
+
     // This field has been removed
     // Since 5.8
     reserved 6;
@@ -929,7 +940,7 @@ message AcquisitionRunInfo {
     // Set information provided by the Bream toolkit.
     BreamInfo bream_info = 15;
 
-    // Target Run-Until Critiera, used to determine when the acquisition should be paused
+    // Target Run-Until Criteria, used to determine when the acquisition should be paused
     // or stopped.
     //
     // Since 5.3
@@ -954,7 +965,10 @@ message SetSignalReaderRequest {
 
     // Available signal reader types
     enum SignalReaderType {
+        option allow_alias = true;
+
         HDF5 = 0; // Default value
+        PLAYBACK = 0; // Renamed default value - playback can handle non-hdf file formats too.
         DEVICE = 1;
     }
 
@@ -977,6 +991,20 @@ message SetSignalReaderRequest {
 
 message SetSignalReaderResponse {}
 
+message GetSignalReaderRequest {}
+message GetSignalReaderResponse {
+    // The type of signal reader to use
+    SetSignalReaderRequest.SignalReaderType reader = 1 [(rpc_required) = true];
+
+    // The following is only set if the signal reader is a playback source.
+    string playback_source = 2;
+
+    SetSignalReaderRequest.SourceFileMode playback_mode = 3;
+
+    float sample_rate_scale_factor = 4;
+}
+
+
 message SetBreamInfoRequest {
     // The information to set.
     //