dtcenter · JohnHalleyGotway · Jan 28, 2021 · Nov 7, 2020 · Nov 7, 2020 · Nov 10, 2020
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -2,17 +2,19 @@
 
 - [ ] Describe testing already performed for these changes:</br>
 
-- [ ] Recommend testing for the reviewer to perform, including the location of input datasets:</br>
+- [ ] Recommend testing for the reviewer(s) to perform, including the location of input datasets, and any additional instructions:</br>
+
+- [ ] Do these changes include sufficient documentation and testing updates? **[Yes or No]**
 
 - [ ] Will this PR result in changes to the test suite? **[Yes or No]**</br>
 If **yes**, describe the new output and/or changes to the existing output:</br>
 
-- [ ] After merging, should the reviewer **DELETE** the feature branch from GitHub? **[Yes or No]**</br>
-
 ## Pull Request Checklist ##
 See the [METplus Workflow](https://dtcenter.github.io/METplus/Contributors_Guide/github_workflow.html) for details.
 - [ ] Complete the PR definition above.
 - [ ] Ensure the PR title matches the feature or bugfix branch name.
 - [ ] Define the PR metadata, as permissions allow.
 Select: **Reviewer(s)**, **Project(s)**, and **Milestone**
 - [ ] After submitting the PR, select **Linked Issues** with the original issue number.
+- [ ] After the PR is approved, merge your changes. If permissions do not allow this, request that the reviewer do the merge.
+- [ ] Close the linked issue and delete your feature or bugfix branch from GitHub.
diff --git a/met/docs/Users_Guide/release-notes.rst b/met/docs/Users_Guide/release-notes.rst
@@ -8,6 +8,21 @@ https://github.com/dtcenter/MET/issues
 Version |version| release notes (|release_date|)
 ------------------------------------------------
 
+- See complete list of `GitHub Issues <https://github.com/NCAR/MET/milestone/68?closed=1>`_.
+- Fix Grid-Diag to correctly ignore missing data values (`#1562 <http://github.com/dtcenter/MET/issues/1562>`_).
+- Fix ncdump in the MET Docker image (`#1554 <http://github.com/dtcenter/MET/issues/1554>`_).
+- Fix bug in the MODE CTS output when running multiple convolution radii and thresholds (`#1547 <http://github.com/dtcenter/MET/issues/1547>`_).
+- Fix Stat-Analysis python embedding when the python script has zero arguments (`#1537 <http://github.com/dtcenter/MET/issues/1537>`_).
+- Fix ascii file list parsing logic (`#1484 <http://github.com/dtcenter/MET/issues/1484>`_).
+- Add support for Gaussian grids in the vx_data2d_python library (`#1477 <http://github.com/dtcenter/MET/issues/1477>`_).
+- Fix Ensemble-Stat logic when multiple ensemble members contain no valid data (`#1475 <http://github.com/dtcenter/MET/issues/1475>`_).
+- Add error message to state that python embedding pickling logic is not yet supported (`#1472 <http://github.com/dtcenter/MET/issues/1472>`_).
+- Fix TC-Gen to correctly handle the lead_window configuration file filtering option (`#1465 <http://github.com/dtcenter/MET/issues/1465>`_).
+- Fix the madis2nc log message for ACARS input, not ACARS profiler input (`#1409 <http://github.com/dtcenter/MET/issues/1409>`_).
+
+Version 9.1 release notes (20200810)
+------------------------------------
+
 - Bugfixes:
    - All changes included in the `met-9.0.1 <https://github.com/dtcenter/MET/milestone/64?closed=1>`_, `met-9.0.2 <https://github.com/dtcenter/MET/milestone/65?closed=1>`_, and `met-9.0.3 <https://github.com/dtcenter/MET/milestone/66?closed=1>`_ bugfix releases.
 

diff --git a/met/docs/conf.py b/met/docs/conf.py
@@ -5,7 +5,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
-
+ 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -20,11 +20,11 @@
 project = 'MET'
 author = 'UCAR/NCAR, NOAA, CSU/CIRA, and CU/CIRES'
 author_list = 'Brown, B., Bullock, R., Fowler, T., Halley Gotway, J., Newman, K., Jensen, T.'
-version = '9.1'
+version = '9.1.1'
 verinfo = version
 release = f'{version}'
 release_year = '2020'
-release_date = f'{release_year}0810'
+release_date = f'{release_year}1118'
 copyright = f'{release_year}, {author}'
 
 # -- General configuration ---------------------------------------------------

diff --git a/met/docs/version b/met/docs/version
diff --git a/met/src/basic/vx_util/data_plane_util.cc b/met/src/basic/vx_util/data_plane_util.cc
@@ -606,7 +606,7 @@ DataPlane subtract(const DataPlane &dp1, const DataPlane &dp2) {
 
 DataPlane normal_cdf(const DataPlane &dp, const DataPlane &mn,
                      const DataPlane &sd) {
-   DataPlane cdf = dp;
+   DataPlane cdf = mn;
    double v;
 
    // Check grid dimensions

diff --git a/met/src/basic/vx_util/util_constants.h b/met/src/basic/vx_util/util_constants.h
@@ -18,6 +18,7 @@
 ////////////////////////////////////////////////////////////////////////
 
 // Released versions of MET
+static const char met_version_9_1_1[] = "V9.1.1";
 static const char met_version_9_1[]   = "V9.1";
 static const char met_version_9_0[]   = "V9.0";
 static const char met_version_8_1[]   = "V8.1";
@@ -38,7 +39,7 @@ static const char met_version_1_1[]   = "V1.1";
 
 ////////////////////////////////////////////////////////////////////////
 
-static const char * const met_version    = met_version_9_1;
+static const char * const met_version    = met_version_9_1_1;
 static const char default_met_data_dir[] = "MET_BASE";
 static const char txt_file_ext[]         = ".txt";
 static const char stat_file_ext[]        = ".stat";

diff --git a/met/src/libcode/vx_data2d_grib2/data2d_grib2.cc b/met/src/libcode/vx_data2d_grib2/data2d_grib2.cc
@@ -930,6 +930,10 @@ void MetGrib2DataFile::read_grib2_record_list() {
 
    }  //  END:  while( read_grib2_record() )
 
+   mlog << Debug(4) << "MetGrib2DataFile::read_grib2_record_list() - "
+        << "processed " << rec_num - 1 << " records from GRIB2 file: "
+        << Filename << "\n";
+
    return;
 }
 

diff --git a/met/src/libcode/vx_series_data/series_pdf.cc b/met/src/libcode/vx_series_data/series_pdf.cc
@@ -66,8 +66,9 @@ void update_pdf(
 
     for(int i = 0; i < dp.nx(); i++) {
         for(int j = 0; j < dp.ny(); j++) {
-            if(!mp.s_is_on(i, j)) continue;
             double value = dp.get(i, j);
+            if(!mp.s_is_on(i, j) ||
+               is_bad_data(value)) continue;
             int k = floor((value - min) / delta);
             if(k < 0) k = 0;
             if(k >= pdf.size()) k = pdf.size() - 1;
@@ -92,12 +93,14 @@ void update_joint_pdf(
 
     for(int i = 0; i < dp_A.nx(); i++) {
         for(int j = 0; j < dp_A.ny(); j++) {
-            if(!mp.s_is_on(i, j)) continue;
             double value_A = dp_A.get(i, j);
+            double value_B = dp_B.get(i, j);
+            if(!mp.s_is_on(i, j)    ||
+               is_bad_data(value_A) ||
+               is_bad_data(value_B)) continue;
             int k_A = floor((value_A - min_A) / delta_A);
             if(k_A < 0) k_A = 0;
             if(k_A >= n_A) k_A = n_A - 1;
-            double value_B = dp_B.get(i, j);
             int k_B = floor((value_B - min_B) / delta_B);
             if(k_B < 0) k_B = 0;
             if(k_B >= n_B) k_B = n_B - 1;

diff --git a/met/src/libcode/vx_statistics/pair_base.cc b/met/src/libcode/vx_statistics/pair_base.cc
@@ -1026,9 +1026,40 @@ NumArray derive_climo_prob(const NumArray &mn_na, const NumArray &sd_na,
    n_mn = mn_na.n_valid();
    n_sd = sd_na.n_valid();
 
-   // For CDP threshold types, the climo_prob is constant.
+   // For CDP threshold types, the climo probability is constant
    if(othresh.get_ptype() == perc_thresh_climo_dist) {
-      climo_prob.add_const(othresh.get_pvalue()/100.0, n_mn);
+
+      // Climo probability varies based on the threshold type
+      switch(othresh.get_type()) {
+
+         case thresh_lt:
+         case thresh_le:
+            prob = othresh.get_pvalue()/100.0;
+            break;
+
+         case thresh_eq:
+            prob = 0.0;
+            break;
+
+         case thresh_ne:
+            prob = 1.0;
+            break;
+
+         case thresh_gt:
+         case thresh_ge:
+            prob = 1.0 - othresh.get_pvalue()/100.0;
+            break;
+
+         default:
+            mlog << Error << "\n\nderive_climo_prob() -> "
+                 << "climatological threshold \"" << othresh.get_str()
+                 << "\" cannot be converted to a probability!\n\n";
+            exit(1);
+            break;
+      }
+
+      // Add constant climo probability value
+      climo_prob.add_const(prob, n_mn);
    }
    // If both mean and standard deviation were provided, use them to
    // derive normal climatological probabilities for the current event

diff --git a/met/src/tools/core/grid_stat/grid_stat.cc b/met/src/tools/core/grid_stat/grid_stat.cc
@@ -1074,7 +1074,7 @@ void process_scores() {
                      conf_info.vx_opt[i].interp_info.field);
          }
          if(conf_info.vx_opt[i].nc_info.do_climo && !cmn_dp.is_empty() && !csd_dp.is_empty()) {
-            write_nc((string)"CLIMO_CDF", normal_cdf(cmn_dp, csd_dp, obs_dp),
+            write_nc((string)"CLIMO_CDF", normal_cdf(obs_dp, cmn_dp, csd_dp),
                      i, mthd, pnts, conf_info.vx_opt[i].interp_info.field);
          }
 

diff --git a/met/src/tools/other/pb2nc/numpbmsg.f b/met/src/tools/other/pb2nc/numpbmsg.f
@@ -24,7 +24,29 @@ SUBROUTINE NUMPBMSG ( FID, NMSG )
 C*
         END
 
-
+
+        SUBROUTINE NUMPBMSG_NEW ( PBFILE, FID, NMSG )
+C*
+        INCLUDE    'readpb.prm'
+C*
+        CHARACTER  PBFILE*(FILEMXSTRL)
+        INTEGER    FID, FID2
+        INTEGER    NMSG
+        REAL*8     R8ARR(1, 1)
+C*
+C-----------------------------------------------------------------------
+C*
+C*      Call UFBTAB to figure out how many messages the PrepBufr file
+C*      attached to FID contains
+C*
+        OPEN  ( UNIT = FID, FILE = PBFILE, FORM = 'UNFORMATTED' )
+        FID2 = -FID
+        CALL UFBTAB  ( FID2, R8ARR, 1, 1, NMSG, ' ' )
+        CLOSE ( UNIT = FID )
+C*
+        END
+
+
         SUBROUTINE GET_TMIN ( FID, TMIN )
 C*
         INTEGER    FID, TMIN

diff --git a/met/src/tools/other/pb2nc/pb2nc.cc b/met/src/tools/other/pb2nc/pb2nc.cc
@@ -312,6 +312,7 @@ static NcFile *f_out      = (NcFile *) 0;
 
 extern "C" {
    void numpbmsg_(int *, int *);
+   void numpbmsg_new_(const char *, int *, int *);
    void openpb_(const char *, int *);
    void closepb_(int *);
    void readpb_(int *, int *, int *, double[mxr8pm],
@@ -2059,14 +2060,14 @@ void process_pbfile_metadata(int i_pb) {
            << "Invalid file ID [" << unit << "] between 1 and 99.\n\n";
    }
 
-   // Open the blocked temp PrepBufr file for reading
-   openpb_(blk_file.c_str(), &unit);
-
    // Compute the number of PrepBufr records in the current file.
-   numpbmsg_(&unit, &npbmsg);
+   numpbmsg_new_(blk_file.c_str(), &unit, &npbmsg);
    mlog << Debug(1) << method_name << " -> "
         << "the number of records: " << npbmsg << "\n";
 
+   // Open the blocked temp PrepBufr file for reading
+   openpb_(blk_file.c_str(), &unit);
+
    // Use the number of records requested by the user if there
    // are enough present.
    if(nmsg >= 0 && nmsg <= npbmsg) {

diff --git a/scripts/docker/Dockerfile b/scripts/docker/Dockerfile
@@ -131,7 +131,7 @@ RUN echo "Downloading HDF4.2r3 from ${HDF4_URL}" \
  && cd /met/external_libs/HDF4.2r3 \
  && LOG_FILE=/met/logs/HDF4.2r3_configure.log \
  && echo "Configuring HDF4.2r3 and writing log file ${LOG_FILE}" \
- && ./configure --prefix=/usr/local --disable-netcdf > ${LOG_FILE} \
+ && ./configure --prefix=/usr/local/hdf --disable-netcdf > ${LOG_FILE} \
  && cat mfhdf/hdiff/Makefile | sed 's/LIBS = -ljpeg -lz/LIBS = -ljpeg -lz -lm/g' > Makefile_NEW \
  && mv -f Makefile_NEW mfhdf/hdiff/Makefile \
  && LOG_FILE=/met/logs/HDF4.2r3_make_install.log \
@@ -142,11 +142,12 @@ RUN echo "Downloading HDF4.2r3 from ${HDF4_URL}" \
  && cd /met/external_libs/hdfeos \
  && LOG_FILE=/met/logs/hdfeos_configure.log \
  && echo "Configuring hdfeos and writing log file ${LOG_FILE}" \
- && ./configure --prefix=/usr/local --with-hdf4=/usr/local CC=/usr/local/bin/h4cc > ${LOG_FILE} \
+ && ./configure --prefix=/usr/local/hdfeos --with-hdf4=/usr/local/hdf CC=/usr/local/hdf/bin/h4cc > ${LOG_FILE} \
  && LOG_FILE=/met/logs/hdfeos_make_install.log \
  && echo "Compiling hdfeos and writing log file ${LOG_FILE}" \
  && make install > ${LOG_FILE} \
- && cp include/*.h /usr/local/include/. \
+ && mkdir /usr/local/hdfeos/include \
+ && cp include/*.h /usr/local/hdfeos/include/. \
  && cd /met/external_libs \
  && rm -rf HDF4.2r3 hdfeos
 
@@ -163,6 +164,7 @@ RUN echo "Checking out MET ${MET_GIT_NAME} from ${MET_GIT_URL}" \
  && ./bootstrap \
  && echo "Configuring MET ${MET_GIT_NAME} and writing log file ${LOG_FILE}" \
  && ./configure --enable-grib2 --enable-mode_graphics --enable-modis --enable-lidar2nc --enable-python \
+    MET_HDF=/usr/local/hdf MET_HDFEOS=/usr/local/hdfeos \
     MET_FREETYPEINC=/usr/include/freetype2 MET_FREETYPELIB=/usr/lib \
     MET_CAIROINC=/usr/include/cairo MET_CAIROLIB=/usr/lib \
     MET_PYTHON_CC='-I/usr/include/python3.6m' MET_PYTHON_LD='-lpython3.6m' > ${LOG_FILE} \

diff --git a/test/config/GridDiagConfig_TMP b/test/config/GridDiagConfig_TMP
@@ -62,7 +62,7 @@ data = {
 
 mask = {
    grid = "";
-   poly = "MET_BASE/poly/CONUS.poly";
+   poly = "";
 }
 
 ////////////////////////////////////////////////////////////////////////////////

diff --git a/test/xml/unit_tc_gen.xml b/test/xml/unit_tc_gen.xml
@@ -22,7 +22,7 @@
       -config &CONFIG_DIR;/TCGenConfig_2016 \
       -out &OUTPUT_DIR;/tc_gen/tc_gen_2016 \
       -log &OUTPUT_DIR;/tc_gen/tc_gen_2016.log \
-      -v 2
+      -v 5 
     </param>
     <output>
       <stat>&OUTPUT_DIR;/tc_gen/tc_gen_2016.stat</stat>