Merge pull request #46 from PPPLDeepLearning/feature/documentation

Improve reproducibility of preprocessing; add ALCF documentation

.travis.yml

@@ -34,12 +34,12 @@ env:
 # before_install:
 
 install:
-  - sh install-mpi.sh
+  - sh ci/travis/install-mpi.sh
   - export MPI_PREFIX="${HOME}/opt/${MPI_LIBRARY}-${MPI_LIBRARY_VERSION}"
   - export PATH="${HOME}/.local/bin:${MPI_PREFIX}/bin${PATH:+":${PATH}"}"
   - export LD_LIBRARY_PATH="${MPI_PREFIX}/lib${LD_LIBRARY_PATH:+":${LD_LIBRARY_PATH}"}"
   - pip install --upgrade pip
-  - pip install -r requirements-travis.txt
+  - pip install -r envs/pip-requirements-travis.txt
 
 # before_script:
 
@@ -54,6 +54,8 @@ stages:
 
 notifications:
   email:
+    recipients:
+      - [email protected]
     on_success: change
     on_failure: always
   slack:

data/signals.py

@@ -85,12 +85,9 @@ def get_units(str):
     if found:
         if rank > 1:
             xdata = c.get('dim_of(_s,1)').data()
-            # xunits = get_units('dim_of(_s,1)')
             ydata = c.get('dim_of(_s)').data()
-            # yunits = get_units('dim_of(_s)')
         else:
             xdata = c.get('dim_of(_s)').data()
-            # xunits = get_units('dim_of(_s)')
 
     # MDSplus seems to return 2-D arrays transposed.  Change them back.
     if np.ndim(data) == 2:
@@ -406,6 +403,11 @@ def fetch_nstx_data(signal_path, shot_num, c):
     # 'tmamp1':tmamp1, 'tmamp2':tmamp2, 'tmfreq1':tmfreq1, 'tmfreq2':tmfreq2,
     # 'pechin':pechin,
     # 'rho_profile_spatial':rho_profile_spatial, 'etemp':etemp,
+    # -----
+    # TODO(KGF): replace this hacky workaround
+    # IMPORTANT: must comment-out the following line when preprocessing for
+    # training on JET CW and testing on JET ILW (FRNN 0D).
+    # Otherwise 1K+ CW shots are excluded due to missing profile data
     'etemp_profile': etemp_profile, 'edens_profile': edens_profile,
     # 'itemp_profile':itemp_profile, 'zdens_profile':zdens_profile,
     # 'trot_profile':trot_profile, 'pthm_profile':pthm_profile,