Merge pull request #14 from Sheshuk/v0.9

Updated for snap_base v2.0 syntax

Author: Sheshuk

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2
@@ -27,8 +27,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest hypothesis pytest-asyncio
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python -m pip install ".[test]"
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

README.md

@@ -12,37 +12,6 @@ This package contains plugins for [SNAP](https://github.com/Sheshuk/snap-base) f
 python -m pip install snap-combine
 ```
 
-## Plugins
-
-This package contains plugins which can be used in new snap pipeline configurations.
-
-#### Monitoring: `snap.util.monitor`
-
-* `tqdm_ticker`: a provides [tqdm](https://github.com/tqdm/tqdm)-based ticker, which counts the data flow and data rate through current step.
-
-#### Generating client data: `snap.client.fake`
-
-* `sample_ts`: Generates the neutrino interaction timestamps, using the given rate. Can simulate the supernova signal at the given time.
-
-#### Processing client data: `snap.client`
-
-* `sigcalc.ShapeAnalysis`: calculate supernova significance using shape analysis
-* `setId`: change the datablock ID
-
-#### Combination: `snap.combine`:
-
-* `Buffer`: accumulate the data to synchrnize before combining
-* `methods.Fisher`:   combine data using Fisher's combination method
-* `methods.Stouffer`: combine data using Stouffer's combination method
-
-#### Triggering: `snap.util.threshold`
-
-* Threshold: select and forward only portions of data with significance above given threshold
-
-#### Misc: `snap.util`
-
-* `dump_to_file`: Dump data to given file
-
 ## Example
 
 Example configurations provided the `examples` dir use these steps to 
@@ -51,17 +20,17 @@ Example configurations provided the `examples` dir use these steps to
 
 On client side run 
 ```
-snap client_sender.yml -n node1
+DETECTOR="det_name_1" snap_run client_sender.yml
 ```
 
-Optionally in another session:
+Optionally in another terminal session:
 ```
-snap client_sender.yml -n node2
+DETECTOR="det_name_2" snap_run client_sender.yml
 ```
 
 In another session (combination side):
 ```
-snap combine.yml
+snap_run combine.yml
 ```
 
 You should see the monitoring ticks for all nodes.

examples/client_sender.yml

@@ -1,42 +1,40 @@
-signal_shapes:
-  - &signal1
-    - [-2.0, 0, 10]
-    - [0,  10,   0]
+config:
+  - &detector_id "${DETECTOR}"
+  - &seconds_to_SN 30
+  - &bg_level 1
+  - signal_shapes:
+    - &signal1
+      - [-2.0, 0, 10]
+      - [0,  10,   0]
 
-  - &signal2
-    - [0,  20]
-    - [20,  0]
+    - &signal2
+      - [0,  20]
+      - [20,  0]
 
 
-node:
-    generate:
-        source: 
-            .client.fake.sample_ts: {B: 1, S: *signal1, tSN: 10}
-        steps:
-            - .client.fake.realtime
-            - .tqdm.counter: {desc: "Data"}
-            - .client.sigcalc.CountAna: { B: 2, time_window: [0,5], dt: 0.1, tChunk_min: 1}
-            - .tqdm.counter: {desc: "DataBlocks"}
-        to: [send]
-    send:
-        steps:
-            - .client.setId: {id: "client1"}
-            - .io.zmq.send: {address: "ipc://ipc_combiner"}
-              
+node: !Node
+    - !chain
+        - !from .client.fake.sample_ts: {B: *bg_level, S: *signal1, tSN: *seconds_to_SN}
+        - .client.fake.realtime: {}
+        - .tqdm.counter: {desc: "Data"}
+        - .client.sigcalc.CountAna: { B: *bg_level, time_window: [0,5], dt: 0.1, tChunk_min: 1}
+        - .tqdm.counter: {desc: "DataBlocks"}
+        - !to Sender
 
-node2:
-    detonate:
-        source:
-            .client.fake.detonator: {delay: 15} 
-        steps:
-            - .timing.every: {seconds: 60}
-            - .output.dump: {prefix: "detonator"}
-        to: generate
+    - !chain:Sender
+        - .client.setId: {id: *detector_id}
+        - .io.zmq.send: {address: "ipc://ipc_combiner"}
+            
 
-    generate:
-        steps:
-            - .client.fake.Generator: {B: 1, S: *signal1}
-            - .client.fake.realtime
-            - .tqdm.counter: {desc: "Data"}
-              #to: process
+node2: !Node
+    - !chain:TimeBomb 
+        - !from .client.fake.detonator: {delay: 15} 
+        - .timing.every: {seconds: 60}
+        - .output.dump: {prefix: "TimeBomb:"}
+        - !to Generate
+
+    - !chain:Generate
+        - .client.fake.Generator: {B: 1, S: *signal1}
+        - .client.fake.realtime
+        - .tqdm.counter: {desc: "Data"}
 

examples/combine.yml

@@ -1,17 +1,13 @@
-node:
-    receive:
-        source: 
-            .io.zmq.recv: {address: "ipc://ipc_combiner"}
-        steps:
-            - .tqdm.counter: {desc: "Data received"}
-            - .output.dump_to_file: {fname: "data_received.dat"}
+node: !Node
+    - !chain
+        - !from .io.zmq.recv: {address: "ipc://ipc_combiner"}
+        - .tqdm.counter: {desc: "Data received"}
+        - .output.dump_to_file: {fname: "data_received.dat"}
+        - !to Combine
 
-            - .combine.Buffer: {delay: 5, timeout: 600}
-            - .combine.methods.Fisher
-            - .tqdm.counter: {desc: "Data combined"}
-            - .output.dump_to_file: {fname: "data_combined.dat"}
-
-            - .process.Threshold: {thr: 5}
-            - .tqdm.counter: {desc: "Triggers"}
-            - .output.dump_to_file: {fname: "data_triggered.dat"}
+    - !chain:Combine
+        - .combine.Buffer: {delay: 5, timeout: 600}
+        - .combine.methods.Fisher
+        - .tqdm.counter: {desc: "Data combined"}
+        - .output.dump_to_file: {fname: "data_combined.dat"}
 

setup.py

@@ -13,10 +13,12 @@
         packages=['snap.elements.combine','snap.elements.process','snap.elements.client'],
         py_modules=['snap.datablock'],
         install_requires=['numpy >= 1.19',
-                          'snap-base[io] >=1.3.3',
-                          'sn_stat==0.3.3',
+                          'snap-base >=2.0.3',
+                          'sn_stat>=0.3.4',
         ],
-        extras_require={'doc':['sphinx', 'sphinx-rtd-theme']},
+        extras_require={'doc':['sphinx', 'sphinx-rtd-theme'],
+                        'test':['flake8','pytest','hypothesis','pytest-asyncio']
+        },
         python_requires='>=3.7'
      )
 

snap/__init__.py

@@ -1 +1 @@
-__version_combine__="0.8"
+__version_combine__="0.9.0"

test/test_databuffer.py

@@ -18,8 +18,6 @@ def test_new_clients(ts):
     assert buf.clients == {d1.id: d1}
     buf.put(d2)
     assert buf.clients == {d.id: d for d in [d1,d2]}
-    with pytest.raises(ValueError):
-        buf.put(d2)
 
 @given(ts=times)
 def test_append_data(ts):