support for python 2.7 (pytrip#653)

* pytest for 2.7 * typo fixed * fixes * fix no nonlocal in py2.7 * python -m for pytest * missing dep added * missing init added * fix no newline in py2.7 * fix write in py2.7 * fix write in py2.7 with decode * add install of vc++9.0 when py2.7 * add windows check in py 2.7 * vcredist2008 * echo GITHUB_WORKSPACE * wget and msiexec * add comments * [build] * add vc++9.0 in full_tests [build] * fix reqs in setup.py [build] * deepsource fixes [build] * fixes * add building wheel for py2.7 [build] * changes * [build] * change name slice * wget tests * remove msiexec logs * wget changes * deepsource fixes * appveyor py2.7 * fixes * fixes [build] Co-authored-by: michal367 <[email protected]>
ljelen · Dec 15, 2021 · 7ebd134 · 7ebd134
1 parent c841bb3
commit 7ebd134
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Showing 8 changed files with 144 additions and 98 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -43,8 +43,12 @@ jobs:
     needs: [initialise]
     strategy:
        matrix:
-         python-version: ['3.5', '3.9', '3.10']
+         python-version: ['2.7', '3.5', '3.9', '3.10']
          platform: [ubuntu-latest, windows-latest]
+         exclude:
+           # skip this config, because it is slow
+           - python-version: '2.7'
+             platform: windows-latest
     steps:
       - uses: actions/checkout@v2
 
@@ -69,7 +73,7 @@ jobs:
 
       - name: Smoke tests
         run: |
-          pytest -k "smoke" tests/
+          python -m pytest -k "smoke" tests/
 
   full_tests:
      # these full tests, being slow are triggered only in following cases:
@@ -83,7 +87,7 @@ jobs:
      needs: [initialise, smoke_test]
      strategy:
        matrix:
-         python-version: ['3.5', '3.6', '3.7', '3.8', '3.9', '3.10']
+         python-version: ['2.7', '3.5', '3.6', '3.7', '3.8', '3.9', '3.10']
          platform: [ubuntu-latest, windows-latest]
      steps:
      - uses: actions/checkout@v2
@@ -92,6 +96,14 @@ jobs:
        with:
          python-version: ${{ matrix.python-version }}
 
+     - name: Install Visual C++ 9.0 for Python 2.7
+       # we download from web.archive.org, because it is not accessible on official microsoft site
+       # https://stackoverflow.com/questions/43645519/microsoft-visual-c-9-0-is-required
+       if: matrix.platform == 'windows-latest' && matrix.python-version == '2.7'
+       run: |
+         C:\msys64\usr\bin\wget.exe --progress=dot:mega --tries=50 'https://web.archive.org/web/20200709160228if_/https://download.microsoft.com/download/7/9/6/796EF2E4-801B-4FC4-AB28-B59FBF6D907B/VCForPython27.msi'
+         msiexec /i VCForPython27.msi /qn
+
      - name: Install dependencies
        run: |
          python --version
@@ -103,7 +115,7 @@ jobs:
 
      - name: Regular tests
        run: |
-          pytest -k "not slow" tests/
+          python -m pytest -k "not slow" tests/
 
   build_wheels_manylinux1:
     # these full tests, being slow are triggered only in following cases:
@@ -117,7 +129,7 @@ jobs:
     needs: [initialise, full_tests]
     strategy:
        matrix:
-         python-versions: ["cp35-cp35m", "cp36-cp36m", "cp37-cp37m","cp38-cp38", "cp39-cp39"]
+         python-versions: ["cp27-cp27m", "cp35-cp35m", "cp36-cp36m", "cp37-cp37m","cp38-cp38", "cp39-cp39"]
 
     steps:
     - uses: actions/checkout@v2

diff --git a/appveyor.yml b/appveyor.yml
@@ -9,6 +9,9 @@ environment:
      secure: GgEHENWgbfFj3Y3ESLvQqfHXKyp2BPy65U8B21ACBOw57Yv/epOgh8bp5tsi4PUa9ZkAIRW8m4GZx5HHm4q36zkXZZaZUZYV3qMRNpoGe/EweEdg8dqjW5wAGQ/bDQgVgfbWzg9o2KwuSFd+j1wLcKEc4ZMcKZvgOQlQQXqVKNB3VpeZftjI14ss1QPFgY4TLpa+bfaH1xHVCT/BKAy7y8wKBfZBvpb4xWOyOKaRKDa1+NOxS8TGYRBThWK6R9/gvXvh9ySzFwUbjCbHdcpK/w==
   PYPIUSER: __token__
   matrix:
+    - platform: x64
+      PYTHON: "C:\\Python27-x64"
+
     - platform: x64
       PYTHON: "C:\\Python35-x64"
 

diff --git a/pytrip/cube.py b/pytrip/cube.py
@@ -21,6 +21,7 @@
 A cube is a 3D object holding data, such as CT Hounsfield units, Dose- or LET values.
 """
 import os
+import io
 import re
 import sys
 import logging
@@ -96,7 +97,7 @@ def __init__(self, cube=None):
             # unique for each CT slice
             self._ct_sop_instance_uid = cube._ct_sop_instance_uid
 
-            self.cube = np.zeros((self.dimz, self.dimy, self.dimx), dtype=cube.pydata_type)
+            self.cube = np.zeros((self.dimz, self.dimy, self.dimx), dtype=cube.pydata_type)  # skipcq PTC-W0052
 
         else:
             import getpass
@@ -745,8 +746,14 @@ def _write_trip_header(self, path):
         else:
             output_str += "z_table no\n"
 
-        with open(path, "w+", newline='\n') as f:
-            f.write(output_str)
+        # for compatibility with python 2.7 we need to use `io.open` instead of `open`,
+        # as `open` function in python 2.7 cannot handle `newline` argument.
+        # This needs to be followed by `decode()`d string being written
+        with io.open(path, "w+", newline='\n') as f:
+            try:
+                f.write(output_str)
+            except TypeError:
+                f.write(output_str.decode())
 
     def _write_trip_data(self, path):
         """ Writes the binary data cube in TRiP98 format to a file.

diff --git a/pytrip/ddd.py b/pytrip/ddd.py
@@ -124,9 +124,9 @@ def load_ddd(self, directory):
                 data = f.read()
             lines = data.split('\n')
             for n, line in enumerate(data.split("\n")):
-                if line.find("energy") is not -1:
+                if line.find("energy") != -1:
                     energy = float(line.split()[1])
-                if line.find('!') is -1 and line.find('#') is -1:
+                if line.find('!') == -1 and line.find('#') == -1:
                     break
             for i in range(n, len(lines)):
                 if len(lines[i]) < 3:

diff --git a/pytrip/tripexecuter/execute.py b/pytrip/tripexecuter/execute.py
@@ -467,21 +467,23 @@ def _compress_files(self, source_dir):
         logger.debug("Compressing files in {:s} to {:s}".format(source_dir, target_path))
         self._info("Compressing files in {:s} to {:s}".format(source_dir, target_path))
 
-        total_size = get_size(source_dir)
-        sum_size = 0
+        # trick for no nonlocal in python 2.7
+        track_progress_info = {
+            "total_size": get_size(source_dir),
+            "sum_size": 0
+        }
 
         def track_progress(tarinfo):
-            nonlocal total_size, sum_size
             if tarinfo.isfile():
-                sum_size += tarinfo.size
-                percentage = int(sum_size / total_size * 100)
+                track_progress_info["sum_size"] += tarinfo.size
+                percentage = int(track_progress_info["sum_size"] / track_progress_info["total_size"] * 100)
                 self._log("Compressing file {} with size {} ({}%)".format(tarinfo.name,
                                                                           human_readable_size(tarinfo.size),
                                                                           percentage))
             return tarinfo
 
         with tarfile.open(target_path, "w:gz") as tar:
-            self._log("Size to compress: {:s}".format(human_readable_size(total_size)))
+            self._log("Size to compress: {:s}".format(human_readable_size(track_progress_info["total_size"])))
             tar.add(source_dir, arcname=dirname, filter=track_progress)
         self._log("Compressing done\n")
 
@@ -510,15 +512,17 @@ def _extract_tarball(self, tgz_path, target_dirpath):
         if os.path.exists(out_dirpath):
             shutil.rmtree(out_dirpath)
 
-        sum_size = 0
+        # trick for no nonlocal in python 2.7
+        track_progress_info = {
+            "sum_size": 0
+        }
 
         def track_progress(members, files_total_size):
-            nonlocal sum_size
             for file in members:
                 yield file
                 if file.isfile():
-                    sum_size += file.size
-                    percentage = int(sum_size / files_total_size * 100)
+                    track_progress_info["sum_size"] += file.size
+                    percentage = int(track_progress_info["sum_size"] / files_total_size * 100)
                     self._log("Extracting file {} with size {} ({}%)".format(file.name,
                                                                              human_readable_size(file.size),
                                                                              percentage))