latest update to fast-magephem-service for SHELLS in github

fast-magephem-service/.gitignore

@@ -5,9 +5,9 @@ core.*
 *~
 *.csv
 *.err
-*.so
 *.o
+python/irene/c/*.so
 python/irene/c/common_include
 python/irene/c/lib
 python/irene/c/models_include
-python/irene/lib
+.dockerconfigjson

fast-magephem-service/Dockerfile

@@ -1,24 +1,36 @@
-#FROM e3-devops.aero.org/ssdhas/python:3.9.13-buster
-FROM python:3.9.13-buster
+FROM python:3.9.17-slim-bookworm
 
 WORKDIR /app
 
+#Removing warning in Jenkins about apt-util not being installed, causing containerization to hang
+ENV DEBIAN_FRONTEND noninteractive
+ENV DEBCONF_NOWARNINGS="yes"
+
+RUN apt-get update && apt-get install -y\
+    build-essential \
+    cmake \
+    gfortran \
+    libboost-all-dev \
+    libopenmpi-dev \
+    googletest \
+    libhdf5-dev \
+    libxerces-c-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY requirements.txt .
+
+RUN pip install --no-cache-dir --upgrade pip setuptools \
+    && pip install --no-cache-dir -r requirements.txt \
+    && pip uninstall -y Flask \
+    && pip install Flask==2.2.3
+
 COPY python /app/python
 COPY python/lib /usr/local/lib64/
 COPY test /app/test
-COPY requirements.txt .
 
+RUN ln -s /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/x86_64-linux-gnu/libhdf5.so.103
 
-#RUN DOW=$(date +%a) \
-RUN apt-get update \
-    && apt-get install -y build-essential \
-    && apt-get install -y libhdf5-dev \
-    && apt-get install -y libxerces-c-dev \
-    && pip3 install --upgrade pip setuptools \
-    && pip3 install -r requirements.txt \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && ln -s /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/x86_64-linux-gnu/libhdf5.so.103
+# Run pytest tests
+RUN pytest /app/test
 
-# Run app.py
 CMD ["python", "/app/python/app.py"]

fast-magephem-service/python/app.py

@@ -11,8 +11,7 @@
     update to python 3.7+ to get fromisoformat
         replace strptime call
         modify OpenAPI YAML file to note time format S(.mmmuuu) instead of S.mmm(uuu)
-    add magephem service for OPQ
-    add magephem service for IGRF, T89
+    add magephem service for T89 (when IRENE C++ code supports it)
 """
 
 import sys

fast-magephem-service/python/fast-magephem.yaml

@@ -30,6 +30,7 @@ paths:
         Supports GDZ, GEO, GSM, GSE, SM, GEI, MAG, SPH.<br>
         Provide input system (fromSys) and list of dates (dates), 
           list of 3-D locations (xIN), and requested output system (outSys).<br>
+        Supports up to 100,000 dates/locations <br>
         Returns same list of dates (dates) and list of 3-D locations (xOUT) in output system.<br>
         dates and xIN lists must have same length. xOUT will have that length as well.<br>
         - GDZ - geodetic as alt (km), latitude (deg), longitude (deg).
@@ -67,6 +68,8 @@ paths:
                 xIN:
                   allOf:
                     - $ref: '#/components/schemas/CoordinateList3D'
+                  minItems: 0
+                  maxItems: 100000
                   description: "list of input 3-D coordinate sets in fromSys (nested list)"
       responses:
         '200':
@@ -83,14 +86,16 @@ paths:
                   xOUT:
                     allOf:
                       - $ref: '#/components/schemas/CoordinateList3D'
+                    minItems: 0
+                    maxItems: 100000
                     description: "list of 3-D coordinate sets in toSys (nested list)"
         '405':
           description: Invalid input
   /magephem:
     post:
       tags:
         - magephem
-      summary: Translate from one 3-D frame to another
+      summary: Compute magnetic ephemeris
       description: |
         compute magnetic ephemeris / coordinates for a list of times and locations<br>
 
@@ -112,6 +117,7 @@ paths:
             time x 3, or time x direciton x 3
           - kext - external field model 'opq' or 'igrf' (=none)
           - outputs - list of coordinates to output (I,Bm,K,Phi,hmin,L,Blocal,MLT,Bmin,BminX,BminY,BminZ)<br>
+        Supports up to 100,000 dates/locations, and up to 25 pitch angles/dirs <br>
         At most one of alpha, dirs is allowed. if neither alpha or dirs is provided, assumes alpha=90
 
 
@@ -147,6 +153,8 @@ paths:
                 X:
                   allOf:
                     - $ref: '#/components/schemas/CoordinateList3D'
+                  minItems: 0
+                  maxItems: 100000
                   description: "list of input 3-D coordinate sets (nested list)"
                 sys:
                   allOf:
@@ -164,21 +172,37 @@ paths:
                       description: scalar input pitch angle
                     - type: array
                       example: [10.0,45.0,90.0]
+                      minItems: 0
+                      maxItems: 25
+                      description: "static list of input pitch angles"
+                      items:
+                        $ref: '#/components/schemas/PitchAngle'
+                    - type: array
+                      example: [[10.0,45.0,90.0],[20.0,55.0,95.0]]
+                      minItems: 0
+                      maxItems: 100000
+                      description: "time-varying list of lists input pitch angles"
                       items:
-                        oneOf:
-                          - $ref: '#/components/schemas/PitchAngle'
-                          - type: array
-                            items:
-                              $ref: '#/components/schemas/PitchAngle'
-                      description: "list of input pitch angles"
+                          type: array
+                          minItems: 0
+                          maxItems: 25
+                          items:
+                            $ref: '#/components/schemas/PitchAngle'
                 dirs:
                   oneOf:
                     - allOf:
                         - $ref: '#/components/schemas/CoordinateList3D'
-                      description: "list of input 3-D coordinate sets (nested list)"
+                      minItems: 0
+                      maxItems: 25
+                      description: "list of static input 3-D coordinate sets (nested list)"
                     - type: array
+                      minItems: 0
+                      maxItems: 100000
                       items:
-                        $ref: '#/components/schemas/CoordinateList3D'
+                        allOf:
+                          - $ref: '#/components/schemas/CoordinateList3D'
+                        minItems: 0
+                        maxItems: 25
                       description: "list of lists of input 3-D coordinate sets (nested nested list)"
                 outputs:
                     type: array
@@ -286,6 +310,8 @@ components:
     DateList:
       # supply "description" via {allOf : [ $ref : #/components/schemas/DateList],description:...}
       type: array
+      minItems: 0
+      maxItems: 100000
       items:
         type: string
         format: date-time
@@ -296,10 +322,10 @@ components:
       example: [[ 100.0, 45.0, -73.0],[ 100.1, 45.2, -73.5]]
       items:
         type: array
+        minItems: 3
+        maxItems: 3
         items:
           format: number
-          minLength: 3
-          maxLength: 3
           example: 100.0
     PitchAngle:
       type: number
@@ -317,4 +343,4 @@ components:
               type: number
               default: -1.0E+30
 
-
+

fast-magephem-service/python/irene/fast_invariants.py

@@ -56,7 +56,7 @@
 assert _slash == '/', "non-linux systems not supported yet"
 _flyin_path = os.path.dirname(os.path.abspath(__file__))
 _NN_files = { # file names by [kext][coord] w/o the final .mat, also w/o _Kp# for t89
-        'opq':{'Phi':'fastPhi_net','hmin':'fast_him_net'},
+        'opq':{'Phi':'fastPhi_net','hmin':'fast_hmin_net'},
         'igrf':{'Phi':'fastPhi_net_igrf','hmin':'fast_hmin_net_igrf'},
         }
 _NNs = {key:{} for key in _NN_files} # nets themselves

fast-magephem-service/requirements.txt

@@ -2,4 +2,6 @@ connexion[swagger-ui]==2.14.1
 numpy==1.22.4
 h5py==3.7.0
 scipy==1.9.3
-flask==2.2.5
+pytest==7.4.0
+xlsxwriter==3.1.2
+matplotlib==3.7.1

fast-magephem-service/test/ssdhas_shared/python/test_utils.py

@@ -5,18 +5,19 @@
 
 import numpy as np
 import datetime as dt
+from pytest import approx
 
 def recursive_equals(a,b,path='/'):
     if isinstance(a,np.ndarray):
         assert isinstance(b,np.ndarray), '%s are not both numpy ndarrays ' % path
         assert len(a.dtype) == len(b.dtype), '%s have different dtype structure' % path
         if len(a.dtype) == 0: # simple array
-            assert np.array_equal(a,b,equal_nan=np.issubdtype(a.dtype,float)), 'arrays %s are not equal ' % path
+            assert np.all_close(a,b,equal_nan=np.issubdtype(a.dtype,float)), 'arrays %s are not equal ' % path
             return True
         else: # structured array
             assert a.dtype.names != b.dtype.names, 'structured arrays %s have different keys ' % path
             for key in a.dtype.names:
-                assert np.array_equal(a[key],b[key],equal_nan=np.issubdtype(a[key].dtype,float)),'arrays %s/%s are not equal' % (path,key)
+                assert np.all_close(a[key],b[key],equal_nan=np.issubdtype(a[key].dtype,float)),'arrays %s/%s are not equal' % (path,key)
             return True
 
     if isinstance(a,dict):
@@ -42,9 +43,14 @@ def recursive_equals(a,b,path='/'):
             assert np.issubdtype(type(b),base),'%s are not both %s' % (path,base.__name__)
             assert np.isscalar(a), 'a is not scalar %s' % path
             assert np.isscalar(b), 'b is not scalar %s' % path
-            if base == float:
-                assert (np.isnan(a) == np.isnan(b)), 'Only one is NaN at %s' % (path)
-            assert a==b, 'a != b at %s' % path
+            if base == float: # special case, handling nan and approximately equal
+                if np.isnan(a):
+                    assert np.isnan(b), 'a is nan, b is not at %s' % (path)
+                else:
+                    assert not np.isnan(b), 'b is nan, a is not at %s' % (path)
+                    assert a==approx(b), 'a != b at %s' % path
+            else: # all other classes require exact equals
+                assert a==b, 'a != b at %s' % path
             return True
 
     assert False, 'Unable to compare %s types %s and %s' % (path,type(a),type(b))