Merge pull request #62 from DiamondLightSource/r2.0 ready for v2.0 re…

…lease.

Brings master branch up to date with r2.0 ready for v2.0 release.

.gitignore

@@ -88,3 +88,7 @@ ENV/
 
 # Rope project settings
 .ropeproject
+
+# Autogenerated mpi shell scripts
+IDSort/src/mpijob.sh
+IDSort/src/mpi4shimOpt.sh

.scrutinizer.yml

@@ -18,6 +18,9 @@ build:
       - sudo apt-get update
       - sudo apt-get -y install libopenmpi-dev
       - sudo apt-get -y install openmpi-bin
+  environment:
+    python:
+      version: "3.7"
 filter:
   excluded_paths:
     - '*/test/*'

.travis.yml

@@ -1,6 +1,6 @@
 language: python
 python:
-  - "2.7"
+  - "3.7"
 
 before_install:
   - sudo apt-get update
@@ -12,7 +12,7 @@ install:
   - pip install coveralls coverage
 
 script:
-  - python -m pytest --cov=IDSort --log-format='%(asctime)s.%(msecs)03d %(filename)-25s %(lineno)4d %(levelname)-8s %(message)s' --log-date-format='%Y-%m-%d %H:%M:%S' IDSort/test
+  - python -m pytest --cov=IDSort --log-format='%(asctime)s.%(msecs)03d %(levelname)8s | %(threadName)s | %(module)s::%(funcName)s::%(lineno)-4d | %(message)s' IDSort/test
 
 after_script:
   - coveralls

IDSort/example_configs/shim.yaml

@@ -0,0 +1,56 @@
+id_setup:
+  periods: 113
+  fullmagdims:
+    - 50.0
+    - 30.0
+    - 5.76
+  hemagdims:
+    - 50.0
+    - 30.0
+    - 4.00
+  htmagdims:
+    - 50.0
+    - 30.0
+    - 1.13
+  poledims:
+    - 30.0
+    - 23.0
+    - 2.95
+  interstice: 0.0625
+  gap: 5.6
+  type: 'Hybrid_Symmetric'
+  name: 'test_cpmu_shim'
+  x:
+    - 0
+    - 0.1
+    - 1
+  z:
+    - 0
+    - 0.1
+    - 1
+  steps: 1
+  endgapsym: 3.0
+  terminalgapsymhyb: 3.0
+  output_filename: 'test_cpmu_shim.json'
+magnets:
+  hmags: '/path/to/Opt-ID/IDSort/data/I03H.sim'
+  hemags: '/path/to/Opt-ID/IDSort/data/I03HEC.sim'
+  htmags: '/path/to/Opt-ID/IDSort/data/I03HTE.sim'
+  vmags: null
+  vemags: null
+  output_filename: 'test_cpmu_shim.mag'
+lookup_generator:
+  random: False
+  output_filename: 'test_cpmu_shim.h5'
+process_genome:
+  readable_genome_file: '/path/to/Opt-ID/IDSort/data/test_data/sort/process_genome_analyse_output/1.12875826e-08_000_7c51ecd01f73.genome.inp'
+mpi_runner_for_shim_opt:
+  iterations: 3
+  setup: 24
+  c: 1
+  e: 0.0
+  max_age: 10
+  scale: 10.0
+  bfield_filename: '/path/to/measured_h5_data'
+  number_of_changes: 2
+  number_of_mutations: 5

IDSort/example_configs/shim_z.yaml

@@ -0,0 +1,57 @@
+id_setup:
+  periods: 113
+  fullmagdims:
+    - 50.0
+    - 30.0
+    - 5.76
+  hemagdims:
+    - 50.0
+    - 30.0
+    - 3.48
+  htmagdims:
+    - 50.0
+    - 30.0
+    - 0.87
+  poledims:
+    - 30.0
+    - 26.0
+    - 2.96
+  interstice: 0.04
+  gap: 5.1
+  type: 'Hybrid_Symmetric'
+  name: 'test_cpmu_shim'
+  x:
+    - -2.0
+    - 2.1
+    - 2.5
+  z:
+    - -0.0
+    - 0.1
+    - 0.1
+  steps: 1
+  endgapsym: 5.0
+  terminalgapsymhyb: 5.0
+  output_filename: 'test_cpmu_shim.json'
+magnets:
+  hmags: '/home/tow31676/id_sort_code/Opt-ID/IDSort/data/I03H.sim'
+  hemags: '/home/tow31676/id_sort_code/Opt-ID/IDSort/data/I03HEC.sim'
+  htmags: '/home/tow31676/id_sort_code/Opt-ID/IDSort/data/I03HTE.sim'
+  vmags: null
+  vemags: null
+  output_filename: 'test_cpmu_shim.mag'
+lookup_generator:
+  random: False
+  output_filename: 'test_cpmu_shim.h5'
+process_genome:
+  readable_genome_file:
+    - '/dls/tmp/tow31676/process_genome_output/1.05309977e-08_000_271af39f14c4.genome.inp'
+mpi_runner_for_shim_opt:
+  iterations: 3
+  setup: 24
+  c: 1
+  e: 0.0
+  max_age: 10
+  scale: 10.0
+  bfield_filename: '/dls/tmp/tow31676/process_genome_output/1.24536593e-08_000_51a7950f9b7f.genome.h5'
+  number_of_changes: 2
+  number_of_mutations: 5

IDSort/example_configs/sort.yaml

@@ -0,0 +1,51 @@
+id_setup:
+  periods: 113
+  fullmagdims:
+    - 50.0
+    - 30.0
+    - 5.76
+  hemagdims:
+    - 50.0
+    - 30.0
+    - 3.48
+  htmagdims:
+    - 50.0
+    - 30.0
+    - 0.87
+  poledims:
+    - 30.0
+    - 26.0
+    - 2.96
+  interstice: 0.04
+  gap: 5.1
+  type: 'Hybrid_Symmetric'
+  name: 'test_cpmu'
+  x:
+    - -2.0
+    - 2.1
+    - 2.5
+  z:
+    - -0.0
+    - 0.1
+    - 0.1
+  steps: 1
+  endgapsym: 5.0
+  terminalgapsymhyb: 5.0
+  output_filename: 'test_cpmu.json'
+magnets:
+  hmags: '/path/to/Opt-ID/IDSort/data/I03H.sim'
+  hemags: '/path/to/Opt-ID/IDSort/data/I03HEC.sim'
+  htmags: '/path/to/Opt-ID/IDSort/data/I03HTE.sim'
+  vmags: null
+  vemags: null
+  output_filename: 'test_cpmu.mag'
+lookup_generator:
+  random: False
+  output_filename: 'test_cpmu.h5'
+mpi_runner:
+  iterations: 3
+  setup: 24
+  c: 1
+  e: 0.0
+  max_age: 10
+  scale: 10.0

IDSort/example_configs/sort_z.yaml

@@ -0,0 +1,51 @@
+id_setup:
+  periods: 113
+  fullmagdims:
+    - 50.0
+    - 30.0
+    - 5.76
+  hemagdims:
+    - 50.0
+    - 30.0
+    - 3.48
+  htmagdims:
+    - 50.0
+    - 30.0
+    - 0.87
+  poledims:
+    - 30.0
+    - 26.0
+    - 2.96
+  interstice: 0.04
+  gap: 5.1
+  type: 'Hybrid_Symmetric'
+  name: 'test_cpmu'
+  x:
+    - -2.0
+    - 2.1
+    - 2.5
+  z:
+    - -0.0
+    - 0.1
+    - 0.1
+  steps: 1
+  endgapsym: 5.0
+  terminalgapsymhyb: 5.0
+  output_filename: 'test_cpmu.json'
+magnets:
+  hmags: '/home/tow31676/id_sort_code/Opt-ID/IDSort/data/I03H.sim'
+  hemags: '/home/tow31676/id_sort_code/Opt-ID/IDSort/data/I03HEC.sim'
+  htmags: '/home/tow31676/id_sort_code/Opt-ID/IDSort/data/I03HTE.sim'
+  vmags: null
+  vemags: null
+  output_filename: 'test_cpmu.mag'
+lookup_generator:
+  random: False
+  output_filename: 'test_cpmu.h5'
+mpi_runner:
+  iterations: 3
+  setup: 24
+  c: 1
+  e: 0.0
+  max_age: 10
+  scale: 10.0

IDSort/src/Opt-ID.py

@@ -12,13 +12,14 @@
 # either express or implied. See the License for the specific 
 # language governing permissions and limitations under the License.
 
+import sys
 import os
-import magnets
-import genome_tools
+
 import random
-from genome_tools import ID_BCell
-import field_generator as fg
-import sys
+
+from .magnets import Magnets, MagLists
+from .genome_tools import ID_BCell
+from .field_generator import write_bfields
 
 E_STAR = 0.0
 M_STAR = 1.0
@@ -48,26 +49,27 @@ def mutations(c, e_star, fitness, scale):
     (options, args) = parser.parse_args()
 
     print("Loading magnets")
-    mags = magnets.Magnets()
+    mags = Magnets()
     mags.load(options.magnets_filename)
 
     if options.build:
+
         for filename in args[1::]:
             print("Processing file %s" % (filename))
             # load the genome
             genome = ID_BCell()
             genome.load(filename)
 
             outfile = os.path.join(args[0], os.path.split(filename)[1]+'.h5')
-            fg.output_fields(outfile, options.id_filename, options.lookup_filename, 
-                              options.magnets_filename, genome.genome);
+            write_bfields(outfile, options.id_filename, options.lookup_filename, options.magnets_filename, genome.genome)
+
         sys.exit(0)
 
     if options.setup > 0:
         print("Running setup")
         for i in range(options.setup):
             # create a fresh maglist
-            maglist = magnets.MagLists(mags)
+            maglist = MagLists(mags)
             maglist.shuffle_all()
             genome = ID_BCell(options.id_filename, options.lookup_filename, options.magnets_filename)
             genome.create(maglist)