debian/changelog

+doris (5.0.3~beta+dfsg-11) unstable; urgency=medium
+
+  * debian/control:
+    - add Replaces/Breaks to python3-doris for version << 5.0.3~beta+dfsg-10
+      (Closes: #934605)
+    - now doris Recommends python3-doris
+    - now python3-doris Depends on doris
+    - dorp gv and gmt from the list of recommended packages of python3-doris
+  * debian/patches:
+    - new 0010-Use-sys.executable.patch and 0011-Fix-doris_config.xml-path.patch
+  * Install doris_config.xml.
+  * Move from experimental to unstable.
+
+ -- Antonio Valentino <antonio.valentino@tiscali.it>  Mon, 12 Aug 2019 16:55:09 +0000
+
 doris (5.0.3~beta+dfsg-10) experimental; urgency=medium
 
   * Set compat to 12.

debian/control

@@ -39,6 +39,7 @@ Depends: ${misc:Depends},
          tcsh | c-shell
 Recommends: gmt,
             gv,
+            python3-doris,
             snaphu
 Suggests: eog,
           imagemagick
@@ -58,9 +59,12 @@ Description: Delft object-oriented radar interferometric software
 Package: python3-doris
 Section: contrib/python
 Architecture: all
+Replaces: doris (<< 5.0.3~beta+dfsg-10)
+Breaks: doris (<< 5.0.3~beta+dfsg-10)
 Depends: ${misc:Depends},
          ${python3:Depends},
          ${shlibs:Depends},
+         doris,
          python3-fastkml,
          python3-fiona,
          python3-gdal,
@@ -70,9 +74,7 @@ Depends: ${misc:Depends},
          python3-scipy,
          python3-shapely,
          gdal-bin
-Recommends: gmt,
-            gv,
-            snaphu
+Recommends: snaphu
 Description: Delft object-oriented radar interferometric software - Python tools
  DORIS is an Interferometric Synthetic Aperture Radar (InSAR) processor
  developed by the Delft Institute of Earth Observation and Space Systems

debian/doris_config.xml

+<paths>
+    <source_path>/usr/lib/python3/dist-packages/doris</source_path>
+    <doris_path>/usr/bin/doris</doris_path>
+    <cpxfiddle_path>debian/patches/0011-Fix-doris_config.xml-path.patch</cpxfiddle_path>
+    <snaphu_path>/usr/bin/snaphu</snaphu_path>
+    <scihub_username></scihub_username>
+    <scihub_password></scihub_password>
+    <usgs_username></usgs_username>
+    <usgs_password></usgs_password>
+</paths>

debian/patches/0008-python3.patch

@@ -39,13 +39,13 @@ Forwarded: https://github.com/TUDelftGeodesy/Doris/issues/8
  doris_stack/main_code/stack.py                     | 14 ++--
  doris_stack/main_code/swath.py                     |  4 +-
  install/init_cfg.py                                | 14 ++--
- prepare_stack/create_datastack_bash.py             | 12 +--
+ prepare_stack/create_datastack_bash.py             |  6 +-
  prepare_stack/create_dem.py                        | 18 ++--
  prepare_stack/create_doris_input_xml.py            | 28 +++----
  prepare_stack/download_sentinel_data_orbits.py     | 48 +++++------
  prepare_stack/prepare_datastack.py                 |  8 +-
  prepare_stack/prepare_datastack_main.py            |  2 +-
- 41 files changed, 383 insertions(+), 382 deletions(-)
+ 41 files changed, 380 insertions(+), 379 deletions(-)
 
 diff --git a/bin/csk_dump_data.py b/bin/csk_dump_data.py
 index ba54ada..f201650 100755
@@ -2009,16 +2009,10 @@ index 29bf004..eb68d4f 100644
          settings.find('.usgs_password').text = user_input
      else:
 diff --git a/prepare_stack/create_datastack_bash.py b/prepare_stack/create_datastack_bash.py
-index 532f25d..19f1832 100644
+index 532f25d..3113004 100644
 --- a/prepare_stack/create_datastack_bash.py
 +++ b/prepare_stack/create_datastack_bash.py
-@@ -36,12 +36,12 @@ class CreateBash(object):
-         f.write('source_path=' + source_path + '\n')
-         f.write('export PYTHONPATH=$source_path:$PYTHONPATH \n')
-         f.write('export PATH=' + doris_folder + ':' + cpxfiddle_folder + ':' + snaphu_folder + ':' + '$PATH \n')
--        f.write('python ' + doris_run_script + ' -p ' + processing + ' \n')
-+        f.write('python3 ' + doris_run_script + ' -p ' + processing + ' \n')
- 
+@@ -41,7 +41,7 @@ class CreateBash(object):
          f.close()
  
          # make sure the file is executable
@@ -2027,12 +2021,7 @@ index 532f25d..19f1832 100644
  
          # Also create a download and dem creation bash script.
          file_path = os.path.join(stack_folder, 'create_dem.sh')
-@@ -54,11 +54,11 @@ class CreateBash(object):
-         f.write('\n')
-         f.write('source_path=' + source_path + '\n')
-         f.write('export PYTHONPATH=$source_path:$PYTHONPATH \n')
--        f.write('python ' + doris_run_script + ' ' + processing + ' SRTM3 \n')
-+        f.write('python3 ' + doris_run_script + ' ' + processing + ' SRTM3 \n')
+@@ -58,7 +58,7 @@ class CreateBash(object):
          f.close()
  
          # make sure the file is executable
@@ -2041,12 +2030,7 @@ index 532f25d..19f1832 100644
  
          file_path = os.path.join(stack_folder, 'download_sentinel.sh')
          f = open(file_path, 'w')
-@@ -70,8 +70,8 @@ class CreateBash(object):
-         f.write('#!/bin/bash \n')
-         f.write('\n')
- 
--        f.write('python ' + doris_run_script + ' ' + processing + ' \n')
-+        f.write('python3 ' + doris_run_script + ' ' + processing + ' \n')
+@@ -74,4 +74,4 @@ class CreateBash(object):
          f.close()
  
          # make sure the file is executable

debian/patches/0010-Use-sys.executable.patch

+From: Antonio Valentino <antonio.valentino@tiscali.it>
+Date: Mon, 12 Aug 2019 15:51:00 +0000
+Subject: Use sys.executable
+
+---
+ doris_stack/main_code/single_master_stack.py | 21 +++++++++++----------
+ doris_stack/main_code/stack.py               |  4 ++--
+ prepare_stack/create_datastack_bash.py       |  6 +++---
+ 3 files changed, 16 insertions(+), 15 deletions(-)
+
+diff --git a/doris_stack/main_code/single_master_stack.py b/doris_stack/main_code/single_master_stack.py
+index 368515b..cf1b101 100644
+--- a/doris_stack/main_code/single_master_stack.py
++++ b/doris_stack/main_code/single_master_stack.py
+@@ -1,4 +1,5 @@
+ import os
++import sys
+ import numpy as np
+ from datetime import datetime
+ from collections import OrderedDict
+@@ -304,12 +305,12 @@ class SingleMaster(object):
+                     os.chdir(path)
+                     if ps is True:
+                         master_file = self.burst_path(key=burst,dat_type='master',full_path=False)
+-                        command1 = 'python -m ' + 'get_winpos' + ' ' + master_file + ' master.res 21 winpos_cc.asc'
++                        command1 = sys.executable + ' -m ' + 'get_winpos' + ' ' + master_file + ' master.res 21 winpos_cc.asc'
+                         job_list1.append({"path": path, "command": command1})
+                         command2 = self.doris_path + ' ' + os.path.join(self.input_files, 'input.coarsecorr')
+                         job_list2.append({"path": path, "command": command2})
+                         if not self.parallel:
+-                            os.system('python -m ' + 'get_winpos' + ' ' + master_file + ' master.res 21 winpos_cc.asc')
++                            os.system(sys.executable + ' -m ' + 'get_winpos' + ' ' + master_file + ' master.res 21 winpos_cc.asc')
+                             os.system(command2)
+                     if ps is False:
+                         command = self.doris_path + ' ' + os.path.join(self.input_files, 'input.coarsecorr')
+@@ -401,7 +402,7 @@ class SingleMaster(object):
+                 slave_deramped = self.burst_path(key=burst, dat_type='slave_deramped', full_path=False)
+ 
+                 if not os.path.exists(os.path.join(path, slave_deramped)):
+-                    command2 = 'python ' + os.path.join(self.function_path, 'do_deramp_SLC.py') + ' ' + slave_file + ' slave.res'
++                    command2 = sys.executable + ' ' + os.path.join(self.function_path, 'do_deramp_SLC.py') + ' ' + slave_file + ' slave.res'
+                     job_list2.append({"path": path, "command": command2})
+                     if not self.parallel:
+                         os.chdir(path)
+@@ -423,7 +424,7 @@ class SingleMaster(object):
+             master_deramped = self.burst_path(key=burst, dat_type='slave_deramped', full_path=False)
+ 
+             if not os.path.exists(os.path.join(path, master_deramped)) or not master:
+-                command1 = 'python ' + os.path.join(self.function_path, 'do_deramp_SLC.py') + ' ' + master_file + ' slave.res'
++                command1 = sys.executable + ' ' + os.path.join(self.function_path, 'do_deramp_SLC.py') + ' ' + master_file + ' slave.res'
+                 job_list1.append({"path": path, "command": command1})
+                 if not self.parallel:
+                     os.chdir(path)
+@@ -469,7 +470,7 @@ class SingleMaster(object):
+                     if not(self.parallel):
+                         os.chdir(path)
+                     if ps == True:
+-                        command1 = 'python -m' + 'get_winpos'  + ' ' + master_file + ' master.res 101 winpos_fine.asc'
++                        command1 = sys.executable + ' -m' + 'get_winpos'  + ' ' + master_file + ' master.res 101 winpos_fine.asc'
+                         job_list1.append({"path": path, "command": command1})
+                         command2 = self.doris_path + ' ' + os.path.join(self.input_files,'input.finecoreg_icc_pointscat')
+                         job_list2.append({"path": path, "command": command2})
+@@ -900,7 +901,7 @@ class SingleMaster(object):
+ 
+                 if not os.path.exists(os.path.join(path, 'slave_rsmp_reramped.raw')):
+                     # If we are before the ESD step and reramp is not jet done.
+-                    command1 = 'python ' + os.path.join(self.function_path, 'do_reramp_SLC.py') + ' slave_rsmp.raw slave.res'
++                    command1 = sys.executable + ' ' + os.path.join(self.function_path, 'do_reramp_SLC.py') + ' slave_rsmp.raw slave.res'
+                     jobList1.append({"path": path, "command": command1})
+                     if not self.parallel:
+                         os.chdir(path)
+@@ -1262,7 +1263,7 @@ class SingleMaster(object):
+                     overlap = burst + '_' + next_burst
+                     ps_select = '1'
+                     master_date = self.master_date
+-                    command = 'python ' + os.path.join(self.function_path, 'ESD_ps_ds.py') + ' ' + stack_folder + ' ' \
++                    command = sys.executable + ' ' + os.path.join(self.function_path, 'ESD_ps_ds.py') + ' ' + stack_folder + ' ' \
+                               + overlap + ' ' + esd_type + ' ' + max_baseline + ' ' + master_date + ' ' + ps_select
+                     jobList.append({"path": stack_folder, "command": command})
+ 
+@@ -1374,7 +1375,7 @@ class SingleMaster(object):
+                     else:
+                         angle_pixel = str(offset / angle)
+                     script = os.path.join(self.function_path, 'correct_ESD.py')
+-                    command = 'python ' + script + ' ' + filename + ' ' + angle_pixel
++                    command = sys.executable + ' ' + script + ' ' + filename + ' ' + angle_pixel
+ 
+                     jobList.append({"path": path, "command": command})
+                     self.stack[date][burst]['slave'].processes['readfiles']['ESD_correct'] = '1'
+@@ -1634,7 +1635,7 @@ class SingleMaster(object):
+                     command1 = self.doris_path + ' ' + os.path.join(self.input_files, 'input.subtrrefdem')
+                     job_list1.append({"path": path, "command": command1})
+                     if network:
+-                        command2 = 'python ' + os.path.join(self.function_path, 'remove_dem_earth_phase.py') + ' ' + \
++                        command2 = sys.executable + ' ' + os.path.join(self.function_path, 'remove_dem_earth_phase.py') + ' ' + \
+                                    self.stack_folder + ' ' + date + ' ' + burst
+                         job_list2.append({"path": path, "command": command2})
+                     if not self.parallel:
+@@ -2028,7 +2029,7 @@ class SingleMaster(object):
+             final_path = os.path.join(path, master_file)
+ 
+             if not os.path.exists(final_path) or overwrite == True:
+-                command1 = 'python ' + os.path.join(self.function_path, 'concatenate_decatenate.py') + ' ' + path \
++                command1 = sys.executable + ' ' + os.path.join(self.function_path, 'concatenate_decatenate.py') + ' ' + path \
+                            + ' concatenate ' + burst_file + ' ' + dt.name + ' ' + multilooked + ' ' + res_type
+                 job_list1.append({"path": path, "command": command1})
+ 
+diff --git a/doris_stack/main_code/stack.py b/doris_stack/main_code/stack.py
+index 71bac02..c30f872 100644
+--- a/doris_stack/main_code/stack.py
++++ b/doris_stack/main_code/stack.py
+@@ -628,7 +628,7 @@ class StackData(object):
+                     self.datastack[date][swath][burst].write(res_name)
+                     if not os.path.exists(res_name) or not os.path.exists(outdata):
+ 
+-                        write_jobs.append('python ' + self.function_path + 'sentinel_dump_data_function.py ' + data + ' ' + res_name + ' ' + outdata)
++                        write_jobs.append(sys.executable + ' ' + self.function_path + 'sentinel_dump_data_function.py ' + data + ' ' + res_name + ' ' + outdata)
+                         burst_num.append(stack_no + '_' + xml_base[6] + '_' + xml_base[15:23])
+ 
+         # Burst are sorted in such a way that mainly read from different data files sorted by burst then swath then date.
+@@ -666,7 +666,7 @@ class StackData(object):
+             shapefile = self.shape_filename
+             pol = self.polarisation[0]
+             overwrite = False
+-            command1 = ('python ' + self.function_path + 'load_shape_unzip.py ' + zipped_folder + ' ' + dest_folder +
++            command1 = (sys.executable + ' ' + self.function_path + 'load_shape_unzip.py ' + zipped_folder + ' ' + dest_folder +
+                         ' ' + shapefile + ' ' + pol + ' ' + str(overwrite))
+             jobList1.append({"path": self.path, "command": command1})
+             if not self.parallel:
+diff --git a/prepare_stack/create_datastack_bash.py b/prepare_stack/create_datastack_bash.py
+index 3113004..ab8bbfb 100644
+--- a/prepare_stack/create_datastack_bash.py
++++ b/prepare_stack/create_datastack_bash.py
+@@ -36,7 +36,7 @@ class CreateBash(object):
+         f.write('source_path=' + source_path + '\n')
+         f.write('export PYTHONPATH=$source_path:$PYTHONPATH \n')
+         f.write('export PATH=' + doris_folder + ':' + cpxfiddle_folder + ':' + snaphu_folder + ':' + '$PATH \n')
+-        f.write('python ' + doris_run_script + ' -p ' + processing + ' \n')
++        f.write(sys.executable + ' ' + doris_run_script + ' -p ' + processing + ' \n')
+ 
+         f.close()
+ 
+@@ -54,7 +54,7 @@ class CreateBash(object):
+         f.write('\n')
+         f.write('source_path=' + source_path + '\n')
+         f.write('export PYTHONPATH=$source_path:$PYTHONPATH \n')
+-        f.write('python ' + doris_run_script + ' ' + processing + ' SRTM3 \n')
++        f.write(sys.executable + ' ' + doris_run_script + ' ' + processing + ' SRTM3 \n')
+         f.close()
+ 
+         # make sure the file is executable
+@@ -70,7 +70,7 @@ class CreateBash(object):
+         f.write('#!/bin/bash \n')
+         f.write('\n')
+ 
+-        f.write('python ' + doris_run_script + ' ' + processing + ' \n')
++        f.write(sys.executable + ' ' + doris_run_script + ' ' + processing + ' \n')
+         f.close()
+ 
+         # make sure the file is executable

debian/patches/0011-Fix-doris_config.xml-path.patch

+From: Antonio Valentino <antonio.valentino@tiscali.it>
+Date: Mon, 12 Aug 2019 18:36:46 +0200
+Subject: Fix doris_config.xml path
+
+---
+ doris_stack/main_code/doris_config.py          | 5 ++++-
+ doris_stack/main_code/grs_config.py            | 5 ++++-
+ install/init_cfg.py                            | 2 +-
+ prepare_stack/create_datastack_bash.py         | 7 +++++--
+ prepare_stack/create_dem.py                    | 7 +++++--
+ prepare_stack/download_sentinel_data_orbits.py | 5 ++++-
+ prepare_stack/prepare_datastack.py             | 5 ++++-
+ 7 files changed, 27 insertions(+), 9 deletions(-)
+
+diff --git a/doris_stack/main_code/doris_config.py b/doris_stack/main_code/doris_config.py
+index 43520b8..f380c00 100644
+--- a/doris_stack/main_code/doris_config.py
++++ b/doris_stack/main_code/doris_config.py
+@@ -10,7 +10,10 @@ class DorisConfig(object):
+ 
+     def __init__(self):
+ 
+-        xml_file = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))), 'install/doris_config.xml')
++        # xml_file = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))), 'install/doris_config.xml')
++        xml_file = os.environ.get('DORIS_CONFIG_FILE', os.path.expanduser('~/.doris_config.xml'))
++        if not os.path.isfile(xml_file):
++            xml_file = '/etc/doris_config.xml'
+         tree = ET.parse(xml_file)
+         settings = tree.getroot()
+ 
+diff --git a/doris_stack/main_code/grs_config.py b/doris_stack/main_code/grs_config.py
+index 80e61fc..0d13a7a 100644
+--- a/doris_stack/main_code/grs_config.py
++++ b/doris_stack/main_code/grs_config.py
+@@ -10,7 +10,10 @@ class GrsConfig(object):
+ 
+     def __init__(self):
+ 
+-        xml_file = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))), 'install/doris_config.xml')
++        # xml_file = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))), 'install/doris_config.xml')
++        xml_file = os.environ.get('DORIS_CONFIG_FILE', os.path.expanduser('~/.doris_config.xml'))
++        if not os.path.isfile(xml_file):
++            xml_file = '/etc/doris_config.xml'
+         tree = ET.parse(xml_file)
+         settings = tree.getroot()
+ 
+diff --git a/install/init_cfg.py b/install/init_cfg.py
+index eb68d4f..46df5bf 100644
+--- a/install/init_cfg.py
++++ b/install/init_cfg.py
+@@ -5,7 +5,7 @@ import os
+ 
+ def init_cfg():
+     template_xml_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'doris_config_template.xml')
+-    xml_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'doris_config.xml')
++    xml_file = 'doris_config.xml'
+     tree = ET.parse(template_xml_file)
+     settings = tree.getroot()
+ 
+diff --git a/prepare_stack/create_datastack_bash.py b/prepare_stack/create_datastack_bash.py
+index ab8bbfb..d926f88 100644
+--- a/prepare_stack/create_datastack_bash.py
++++ b/prepare_stack/create_datastack_bash.py
+@@ -12,8 +12,11 @@ class CreateBash(object):
+ 
+     def create(self, stack_folder, root_folder, nodes):
+ 
+-        xml_file = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
+-                                'install/doris_config.xml')
++        # xml_file = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
++        #                         'install/doris_config.xml')
++        xml_file = os.environ.get('DORIS_CONFIG_FILE', os.path.expanduser('~/.doris_config.xml'))
++        if not os.path.isfile(xml_file):
++            xml_file = '/etc/doris_config.xml'
+         tree = ET.parse(xml_file)
+         settings = tree.getroot()
+ 
+diff --git a/prepare_stack/create_dem.py b/prepare_stack/create_dem.py
+index 233e730..184b997 100644
+--- a/prepare_stack/create_dem.py
++++ b/prepare_stack/create_dem.py
+@@ -755,8 +755,11 @@ if __name__ == "__main__":
+     tree_stack = ET.parse(xml_file)
+     settings_stack = tree_stack.getroot()[0]
+ 
+-    xml_file = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'install',
+-                                 'doris_config.xml')
++    # xml_file = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'install',
++    #                              'doris_config.xml')
++    xml_file = os.environ.get('DORIS_CONFIG_FILE', os.path.expanduser('~/.doris_config.xml'))
++    if not os.path.isfile(xml_file):
++        xml_file = '/etc/doris_config.xml'
+     print('reading xml file settings doris ' + xml_file)
+     tree_doris = ET.parse(xml_file)
+     settings_doris = tree_doris.getroot()
+diff --git a/prepare_stack/download_sentinel_data_orbits.py b/prepare_stack/download_sentinel_data_orbits.py
+index a434ef5..4b86990 100644
+--- a/prepare_stack/download_sentinel_data_orbits.py
++++ b/prepare_stack/download_sentinel_data_orbits.py
+@@ -448,7 +448,10 @@ if __name__ == "__main__":
+ 
+     # user settings
+     xml_name = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+-    config_xml_file = os.path.join(os.path.join(xml_name, 'install', 'doris_config.xml'))
++    # config_xml_file = os.path.join(os.path.join(xml_name, 'install', 'doris_config.xml'))
++    config_xml_file = os.environ.get('DORIS_CONFIG_FILE', os.path.expanduser('~/.doris_config.xml'))
++    if not os.path.isfile(config_xml_file):
++        config_xml_file = '/etc/doris_config.xml'
+     print('reading xml file settings doris ' + config_xml_file)
+     tree = ET.parse(config_xml_file)
+     settings = tree.getroot()
+diff --git a/prepare_stack/prepare_datastack.py b/prepare_stack/prepare_datastack.py
+index d71a817..ed42bfc 100644
+--- a/prepare_stack/prepare_datastack.py
++++ b/prepare_stack/prepare_datastack.py
+@@ -35,7 +35,10 @@ class PrepareDatastack(object):
+                 os.mkdir(os.path.join(doris_input_xml.get_value('datastack_folder'), foldername))
+ 
+         # Then create the dem file
+-        password_file = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),'install', 'doris_config.xml')
++        # password_file = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),'install', 'doris_config.xml')
++        password_file = os.environ.get('DORIS_CONFIG_FILE', os.path.expanduser('~/.doris_config.xml'))
++        if not os.path.isfile(password_file):
++            password_file = '/etc/doris_config.xml'
+         tree_doris = ET.parse(password_file)
+         settings_doris = tree_doris.getroot()
+         srtm_username = settings_doris.find('.usgs_username').text

debian/patches/series

@@ -7,3 +7,5 @@
 0007-drop-the-install-package.patch
 0008-python3.patch
 0009-Python-doris-package.patch
+0010-Use-sys.executable.patch
+0011-Fix-doris_config.xml-path.patch

debian/python3-doris.install

 usr/lib/python*
 install/init_cfg.py usr/share/doris
 install/*.xml usr/share/doris
+debian/doris_config.xml /etc