Merge pull request #21 from slaclab/development

Development into main
slaclab · Feb 20, 2024 · e49943f · e49943f
2 parents e07def8 + 8fad691
commit e49943f
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diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -22,6 +22,6 @@ jobs:
         pip install scipy
         pip install statsmodels
 
-#   - name: Run tests
-#     run: |
-#       pytest tests/test_FitFunctions.py
+    - name: Run tests
+      run: |
+        pytest tests/test_FitFunctions.py
diff --git a/README.md b/README.md
@@ -1,9 +1,39 @@
 # beamtime-calibration-suite
 [![Build Status](https://github.com/slaclab/beamtime-calibration-suite/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/slaclab/beamtime-calibration-suite/actions/workflows/run-tests.yml)
 
-To run tests:   
-ssh into psana  
-source /sdf/group/lcls/ds/ana/sw/conda2/manage/bin/psconda.sh  
-clone this repo  
-cd beamtime-calibration-suite/tests  
-pytest .  
+To run any suite_scripts or use the library in scripts outside the project directory, you need to append the project directory to your PYTHONPATH, for example:
+export PYTHONPATH="${PYTHONPATH}:~/beamtime_slaclab/beamtime-calibration-suite"
+
+(can add this to your ~/.bashrc so persists between terminal sessions. Library can later have
+a better release method than cloning and adding to path (pip?))
+
+File organization: 
+/calibrationSuite: The library code lives here, and the functions can be imported into other scripts as such:
+
+from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.fitFunctions import *
+from calibrationSuite.Stats import *
+from calibrationSuite.cluster import *
+
+(documentation on the library functionality is still to come, but example usage is seen in the /suite_scripts folder)
+
+/suite_scripts: scripts that use the calibrationSuite library code
+
+/standalone_scripts: scripts that do not use the calibrationSuite library code
+
+/tests: tests files, can be ran with 'pytest .' from the root project directory
+(Currently only test for the fitFunctions libraryh file is running, more tests are to be added)
+
+
+Current Status:
+
+main branch tag v1.0.0 are the scripts used for the 2/17/24 beamtime 
+    -only changes made are to file organization, and to import statements so work with new organization
+    -large changes will be merged into ontop of this, but original scripts can be accessed by checking out this tag
+    -future beamtimes can be tagged as well
+
+Developers:
+
+If you are new to git/github, start here: https://confluence.slac.stanford.edu/pages/viewpage.action?pageId=428802060
+
+Then read the following for an overview of the development process: https://confluence.slac.stanford.edu/pages/viewpage.action?pageId=429562464
diff --git a/standalone_scripts/Stats.py → calibrationSuite/Stats.py b/standalone_scripts/Stats.py → calibrationSuite/Stats.py
diff --git a/standalone_scripts/cluster.py → calibrationSuite/cluster.py b/standalone_scripts/cluster.py → calibrationSuite/cluster.py
diff --git a/standalone_scripts/AnalyzeH5.py → suite_scripts/AnalyzeH5.py b/standalone_scripts/AnalyzeH5.py → suite_scripts/AnalyzeH5.py
@@ -1,6 +1,6 @@
 import h5py
 import numpy as np
-import fitFunctions, ancillaryMethods
+import calibrationSuite.fitFunctions, calibrationSuite.ancillaryMethods
 ##import seaborn as sns
 import matplotlib.pyplot as plt
 from matplotlib.ticker import AutoMinorLocator

diff --git a/suite_scripts/CalcNoise.py b/suite_scripts/CalcNoise.py
@@ -1,5 +1,5 @@
 from calibrationSuite.basicSuiteScript import *
-import Stats
+import calibrationSuite.Stats
 
 class CalcNoise(BasicSuiteScript):
     def __init__(self):

diff --git a/suite_scripts/CalcNoiseAndMean.py b/suite_scripts/CalcNoiseAndMean.py
@@ -1,5 +1,5 @@
 from calibrationSuite.basicSuiteScript import *
-import Stats
+import calibrationSuite.Stats
 
 class CalcNoise(BasicSuiteScript):
     def __init__(self):

diff --git a/suite_scripts/SimpleClustersParallel.py b/suite_scripts/SimpleClustersParallel.py
@@ -1,5 +1,5 @@
 from calibrationSuite.basicSuiteScript import *
-from cluster import Cluster, BuildClusters
+from calibrationSuite.cluster import Cluster, BuildClusters
 
 class SimpleClusters(BasicSuiteScript):
     def __init__(self):

diff --git a/standalone_scripts/analyze_npy.py → suite_scripts/analyze_npy.py b/standalone_scripts/analyze_npy.py → suite_scripts/analyze_npy.py
@@ -1,6 +1,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
-import fitFunctions, ancillaryMethods
+import calibrationSuite.fitFunctions, calibrationSuite.ancillaryMethods
 import sys
 
 class AnalyzeLinearity(object):

diff --git a/tests/OffXavierV4_2.npy → tests/disabled/OffXavierV4_2.npy b/tests/OffXavierV4_2.npy → tests/disabled/OffXavierV4_2.npy
diff --git a/tests/XavierV4_2.npy → tests/disabled/XavierV4_2.npy b/tests/XavierV4_2.npy → tests/disabled/XavierV4_2.npy
diff --git a/tests/test_AnalyzeH5.py → tests/disabled/disabled_test_AnalyzeH5.py b/tests/test_AnalyzeH5.py → tests/disabled/disabled_test_AnalyzeH5.py
diff --git a/tests/test_EventScanParallelSlice.py → ...d/disabled_test_EventScanParallelSlice.py b/tests/test_EventScanParallelSlice.py → ...d/disabled_test_EventScanParallelSlice.py
diff --git a/.../AnalyzeH5_r666_c0_r1_c14_testLabel_E.png → .../AnalyzeH5_r666_c0_r1_c14_testLabel_E.png b/.../AnalyzeH5_r666_c0_r1_c14_testLabel_E.png → .../AnalyzeH5_r666_c0_r1_c14_testLabel_E.png
diff --git a/...zeH5_r666_c0_r1_c14_testLabel_fitInfo.npy → ...zeH5_r666_c0_r1_c14_testLabel_fitInfo.npy b/...zeH5_r666_c0_r1_c14_testLabel_fitInfo.npy → ...zeH5_r666_c0_r1_c14_testLabel_fitInfo.npy
diff --git a/...xpected/AnalyzeH5_r666_c0_testLabel_E.png → ...xpected/AnalyzeH5_r666_c0_testLabel_E.png b/...xpected/AnalyzeH5_r666_c0_testLabel_E.png → ...xpected/AnalyzeH5_r666_c0_testLabel_E.png
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diff --git a/...eExpected/EventScanParallel_c0_r349_n1.h5 → ...eExpected/EventScanParallel_c0_r349_n1.h5 b/...eExpected/EventScanParallel_c0_r349_n1.h5 → ...eExpected/EventScanParallel_c0_r349_n1.h5
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