Merge pull request #130 from jonwright/master

make it pip installable with --editable
FABLE-3DXRD · Apr 8, 2021 · 57a39f4 · 57a39f4
2 parents d472d1a + 6ed24d9
commit 57a39f4
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Showing 119 changed files with 133 additions and 83 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -31,15 +31,16 @@ jobs:
           command: |
             python3 -m venv venv
             . venv/bin/activate
-            pip install six numpy scipy fabio pillow matplotlib pyopengl xfab pyopengltk h5py PyCifRW
-            python setup.py build install
+            python3 -m pip install pip setuptools --upgrade
+            python3 -m pip install pytest numpy
+            python3 -m pip install --editable .
 
       - save_cache:
           key:  ImageD11-{{arch}}-{{ checksum "setup.py" }}
           paths:
             - ./venv
 
-      # run tests!
+      # run tests
       # this example uses Django's built-in test-runner
       # other common Python testing frameworks include pytest and nose
       # https://pytest.org
@@ -48,8 +49,7 @@ jobs:
           name: run tests
           command: |
             . venv/bin/activate
-            cd test
-            python run_tests.py 
+            python3 -m pytest
 
       - store_artifacts:
           path: test-reports

diff --git a/.travis.yml b/.travis.yml
@@ -8,8 +8,9 @@ jobs:
       osx_image: xcode11.2  # Python 3.7.4 running on macOS 10.14.4
       language: shell       # 'language: python' is an error on Travis CI macOS
 install: 
-  - pip3 install --upgrade pip  # all three OSes agree about 'pip3'
-  - pip3 install .
+  - pip3 install --upgrade pip setuptools  # all three OSes agree about 'pip3'
+  - pip3 install pytest numpy
+  - pip3 install --editable .
 # 'python3' is a 'command not found' error on Windows but 'py' works on Windows only
 script: 
-  - cd test && OMP_NUM_THREADS=2 python3 run_tests.py
+  - OMP_NUM_THREADS=2 python3 -m pytest
diff --git a/ImageD11src/ImageD11_file_series.py → ImageD11/ImageD11_file_series.py b/ImageD11src/ImageD11_file_series.py → ImageD11/ImageD11_file_series.py
diff --git a/ImageD11src/ImageD11_thread.py → ImageD11/ImageD11_thread.py b/ImageD11src/ImageD11_thread.py → ImageD11/ImageD11_thread.py
diff --git a/ImageD11src/ImageD11options.py → ImageD11/ImageD11options.py b/ImageD11src/ImageD11options.py → ImageD11/ImageD11options.py
diff --git a/ImageD11src/__init__.py → ImageD11/__init__.py b/ImageD11src/__init__.py → ImageD11/__init__.py
diff --git a/ImageD11src/blobcorrector.py → ImageD11/blobcorrector.py b/ImageD11src/blobcorrector.py → ImageD11/blobcorrector.py
diff --git a/ImageD11src/cImageD11.py → ImageD11/cImageD11.py b/ImageD11src/cImageD11.py → ImageD11/cImageD11.py
@@ -1,9 +1,23 @@
 
 
-# check for avx2 and import cImageD11 module
+# import cImageD11 compiled module and patch the docstrings
+
+import sys
 import struct
 from ImageD11 import cImageD11_docstrings
-from ImageD11._cImageD11 import *
+
+try:
+    from ImageD11._cImageD11 import *
+except ImportError:
+    print("Failed to import compiled C code for cImageD11 module")
+    print("Are you running from a source directory?")
+    print("Try something like:")
+    print("   python -m pip install --editable .")
+    print("or:")
+    print("   python setup.py develop")
+    print("or:")
+    print("   python setup.py build_ext --inplace")
+    sys.exit()
 
 # For 32 or 64 bits
 nbyte = struct.calcsize("P") # 4 or 8

diff --git a/ImageD11src/cImageD11_docstrings.py → ImageD11/cImageD11_docstrings.py b/ImageD11src/cImageD11_docstrings.py → ImageD11/cImageD11_docstrings.py
diff --git a/ImageD11src/columnfile.py → ImageD11/columnfile.py b/ImageD11src/columnfile.py → ImageD11/columnfile.py
diff --git a/ImageD11src/compute_fazit.py → ImageD11/compute_fazit.py b/ImageD11src/compute_fazit.py → ImageD11/compute_fazit.py
diff --git a/ImageD11src/correct.py → ImageD11/correct.py b/ImageD11src/correct.py → ImageD11/correct.py
diff --git a/ImageD11src/depreciated/GE_script.py → ImageD11/depreciated/GE_script.py b/ImageD11src/depreciated/GE_script.py → ImageD11/depreciated/GE_script.py
diff --git a/ImageD11src/depreciated/ImageD11Server.py → ImageD11/depreciated/ImageD11Server.py b/ImageD11src/depreciated/ImageD11Server.py → ImageD11/depreciated/ImageD11Server.py
diff --git a/ImageD11src/depreciated/data.py → ImageD11/depreciated/data.py b/ImageD11src/depreciated/data.py → ImageD11/depreciated/data.py
diff --git a/ImageD11src/depreciated/fft_index.py → ImageD11/depreciated/fft_index.py b/ImageD11src/depreciated/fft_index.py → ImageD11/depreciated/fft_index.py
diff --git a/ImageD11src/depreciated/filterout.py → ImageD11/depreciated/filterout.py b/ImageD11src/depreciated/filterout.py → ImageD11/depreciated/filterout.py
diff --git a/ImageD11src/depreciated/findreflections.py → ImageD11/depreciated/findreflections.py b/ImageD11src/depreciated/findreflections.py → ImageD11/depreciated/findreflections.py
diff --git a/ImageD11src/depreciated/fitgrainxy.py → ImageD11/depreciated/fitgrainxy.py b/ImageD11src/depreciated/fitgrainxy.py → ImageD11/depreciated/fitgrainxy.py
diff --git a/ImageD11src/depreciated/fsrc/bld.bat → ImageD11/depreciated/fsrc/bld.bat b/ImageD11src/depreciated/fsrc/bld.bat → ImageD11/depreciated/fsrc/bld.bat
diff --git a/...11src/depreciated/fsrc/cImageD11_wrap.pyx → ImageD11/depreciated/fsrc/cImageD11_wrap.pyx b/...11src/depreciated/fsrc/cImageD11_wrap.pyx → ImageD11/depreciated/fsrc/cImageD11_wrap.pyx
diff --git a/ImageD11src/depreciated/fsrc/fImageD11.f90 → ImageD11/depreciated/fsrc/fImageD11.f90 b/ImageD11src/depreciated/fsrc/fImageD11.f90 → ImageD11/depreciated/fsrc/fImageD11.f90
diff --git a/...c/depreciated/fsrc/fImageD11_testprog.f90 → ...1/depreciated/fsrc/fImageD11_testprog.f90 b/...c/depreciated/fsrc/fImageD11_testprog.f90 → ...1/depreciated/fsrc/fImageD11_testprog.f90
diff --git a/...D11src/depreciated/fsrc/fImageD11module.c → ImageD11/depreciated/fsrc/fImageD11module.c b/...D11src/depreciated/fsrc/fImageD11module.c → ImageD11/depreciated/fsrc/fImageD11module.c
diff --git a/ImageD11src/depreciated/fsrc/setup.py → ImageD11/depreciated/fsrc/setup.py b/ImageD11src/depreciated/fsrc/setup.py → ImageD11/depreciated/fsrc/setup.py
diff --git a/ImageD11src/depreciated/fsrc/test_cf.py → ImageD11/depreciated/fsrc/test_cf.py b/ImageD11src/depreciated/fsrc/test_cf.py → ImageD11/depreciated/fsrc/test_cf.py
diff --git a/ImageD11src/depreciated/fsrc/test_xlylzl.py → ImageD11/depreciated/fsrc/test_xlylzl.py b/ImageD11src/depreciated/fsrc/test_xlylzl.py → ImageD11/depreciated/fsrc/test_xlylzl.py
diff --git a/...eD11src/depreciated/fsrc/test_xlylzl_c.py → ImageD11/depreciated/fsrc/test_xlylzl_c.py b/...eD11src/depreciated/fsrc/test_xlylzl_c.py → ImageD11/depreciated/fsrc/test_xlylzl_c.py
diff --git a/ImageD11src/depreciated/fsrc/tst.py → ImageD11/depreciated/fsrc/tst.py b/ImageD11src/depreciated/fsrc/tst.py → ImageD11/depreciated/fsrc/tst.py
diff --git a/ImageD11src/depreciated/guifactors.py → ImageD11/depreciated/guifactors.py b/ImageD11src/depreciated/guifactors.py → ImageD11/depreciated/guifactors.py
diff --git a/ImageD11src/depreciated/hist.c → ImageD11/depreciated/hist.c b/ImageD11src/depreciated/hist.c → ImageD11/depreciated/hist.c
diff --git a/ImageD11src/depreciated/hist.py → ImageD11/depreciated/hist.py b/ImageD11src/depreciated/hist.py → ImageD11/depreciated/hist.py
diff --git a/ImageD11src/depreciated/linearity.py → ImageD11/depreciated/linearity.py b/ImageD11src/depreciated/linearity.py → ImageD11/depreciated/linearity.py
diff --git a/scripts/mar2bruker.py → ImageD11/depreciated/mar2bruker.py b/scripts/mar2bruker.py → ImageD11/depreciated/mar2bruker.py
diff --git a/ImageD11src/depreciated/marccd.py → ImageD11/depreciated/marccd.py b/ImageD11src/depreciated/marccd.py → ImageD11/depreciated/marccd.py
diff --git a/ImageD11src/depreciated/opendata.py → ImageD11/depreciated/opendata.py b/ImageD11src/depreciated/opendata.py → ImageD11/depreciated/opendata.py
diff --git a/ImageD11src/depreciated/rebin2d.py → ImageD11/depreciated/rebin2d.py b/ImageD11src/depreciated/rebin2d.py → ImageD11/depreciated/rebin2d.py
diff --git a/ImageD11src/depreciated/recoveromega.py → ImageD11/depreciated/recoveromega.py b/ImageD11src/depreciated/recoveromega.py → ImageD11/depreciated/recoveromega.py
diff --git a/ImageD11src/depreciated/scalem.py → ImageD11/depreciated/scalem.py b/ImageD11src/depreciated/scalem.py → ImageD11/depreciated/scalem.py
diff --git a/ImageD11src/depreciated/scriptable_gui.py → ImageD11/depreciated/scriptable_gui.py b/ImageD11src/depreciated/scriptable_gui.py → ImageD11/depreciated/scriptable_gui.py
diff --git a/ImageD11src/depreciated/test_f2py.py → ImageD11/depreciated/test_f2py.py b/ImageD11src/depreciated/test_f2py.py → ImageD11/depreciated/test_f2py.py
diff --git a/ImageD11src/depreciated/ubitool.py → ImageD11/depreciated/ubitool.py b/ImageD11src/depreciated/ubitool.py → ImageD11/depreciated/ubitool.py
diff --git a/ImageD11src/depreciated/xml_pks.py → ImageD11/depreciated/xml_pks.py b/ImageD11src/depreciated/xml_pks.py → ImageD11/depreciated/xml_pks.py
diff --git a/ImageD11src/eps_sig_solver.py → ImageD11/eps_sig_solver.py b/ImageD11src/eps_sig_solver.py → ImageD11/eps_sig_solver.py
diff --git a/ImageD11src/fft_index_refac.py → ImageD11/fft_index_refac.py b/ImageD11src/fft_index_refac.py → ImageD11/fft_index_refac.py
diff --git a/ImageD11src/finite_strain.py → ImageD11/finite_strain.py b/ImageD11src/finite_strain.py → ImageD11/finite_strain.py
diff --git a/ImageD11src/grain.py → ImageD11/grain.py b/ImageD11src/grain.py → ImageD11/grain.py
diff --git a/ImageD11src/grid_index_parallel.py → ImageD11/grid_index_parallel.py b/ImageD11src/grid_index_parallel.py → ImageD11/grid_index_parallel.py
diff --git a/ImageD11src/guicommand.py → ImageD11/guicommand.py b/ImageD11src/guicommand.py → ImageD11/guicommand.py
diff --git a/ImageD11src/gv_general.py → ImageD11/gv_general.py b/ImageD11src/gv_general.py → ImageD11/gv_general.py
diff --git a/ImageD11src/indexer.py → ImageD11/indexer.py b/ImageD11src/indexer.py → ImageD11/indexer.py
diff --git a/ImageD11src/indexing.py → ImageD11/indexing.py b/ImageD11src/indexing.py → ImageD11/indexing.py
diff --git a/ImageD11src/labelimage.py → ImageD11/labelimage.py b/ImageD11src/labelimage.py → ImageD11/labelimage.py
diff --git a/ImageD11src/lattice_reduction.py → ImageD11/lattice_reduction.py b/ImageD11src/lattice_reduction.py → ImageD11/lattice_reduction.py
diff --git a/ImageD11src/license.py → ImageD11/license.py b/ImageD11src/license.py → ImageD11/license.py
diff --git a/ImageD11src/nbGui/__init__.py → ImageD11/nbGui/__init__.py b/ImageD11src/nbGui/__init__.py → ImageD11/nbGui/__init__.py
diff --git a/ImageD11src/nbGui/fit_cen_trans.ipynb → ImageD11/nbGui/fit_cen_trans.ipynb b/ImageD11src/nbGui/fit_cen_trans.ipynb → ImageD11/nbGui/fit_cen_trans.ipynb
diff --git a/ImageD11src/nbGui/fit_geometry.py → ImageD11/nbGui/fit_geometry.py b/ImageD11src/nbGui/fit_geometry.py → ImageD11/nbGui/fit_geometry.py
diff --git a/ImageD11src/nbGui/test_gui_fit.ipynb → ImageD11/nbGui/test_gui_fit.ipynb b/ImageD11src/nbGui/test_gui_fit.ipynb → ImageD11/nbGui/test_gui_fit.ipynb
diff --git a/ImageD11src/parameters.py → ImageD11/parameters.py b/ImageD11src/parameters.py → ImageD11/parameters.py
diff --git a/ImageD11src/peakmerge.py → ImageD11/peakmerge.py b/ImageD11src/peakmerge.py → ImageD11/peakmerge.py
diff --git a/ImageD11src/peaksearcher.py → ImageD11/peaksearcher.py b/ImageD11src/peaksearcher.py → ImageD11/peaksearcher.py
diff --git a/...ject/make_h5_project_fails_no_external.py → ...ject/make_h5_project_fails_no_external.py b/...ject/make_h5_project_fails_no_external.py → ...ject/make_h5_project_fails_no_external.py
diff --git a/ImageD11src/project/plan_new_peaksearch.md → ImageD11/project/plan_new_peaksearch.md b/ImageD11src/project/plan_new_peaksearch.md → ImageD11/project/plan_new_peaksearch.md
diff --git a/ImageD11src/project/project.py → ImageD11/project/project.py b/ImageD11src/project/project.py → ImageD11/project/project.py
diff --git a/ImageD11src/project/project_yaml.py → ImageD11/project/project_yaml.py b/ImageD11src/project/project_yaml.py → ImageD11/project/project_yaml.py
diff --git a/ImageD11src/project/projects.py → ImageD11/project/projects.py b/ImageD11src/project/projects.py → ImageD11/project/projects.py
diff --git a/ImageD11src/project/test_json.py → ImageD11/project/test_json.py b/ImageD11src/project/test_json.py → ImageD11/project/test_json.py
diff --git a/ImageD11src/rc_array.py → ImageD11/rc_array.py b/ImageD11src/rc_array.py → ImageD11/rc_array.py
diff --git a/ImageD11src/refinegrains.py → ImageD11/refinegrains.py b/ImageD11src/refinegrains.py → ImageD11/refinegrains.py
diff --git a/ImageD11src/rotdex.py → ImageD11/rotdex.py b/ImageD11src/rotdex.py → ImageD11/rotdex.py
diff --git a/ImageD11src/rsv.py → ImageD11/rsv.py b/ImageD11src/rsv.py → ImageD11/rsv.py
diff --git a/ImageD11src/rsv_mapper.py → ImageD11/rsv_mapper.py b/ImageD11src/rsv_mapper.py → ImageD11/rsv_mapper.py
diff --git a/ImageD11src/saintraw.py → ImageD11/saintraw.py b/ImageD11src/saintraw.py → ImageD11/saintraw.py
diff --git a/ImageD11src/scale.py → ImageD11/scale.py b/ImageD11src/scale.py → ImageD11/scale.py
diff --git a/ImageD11src/silxGui/__init__.py → ImageD11/silxGui/__init__.py b/ImageD11src/silxGui/__init__.py → ImageD11/silxGui/__init__.py
diff --git a/ImageD11src/silxGui/readme.md → ImageD11/silxGui/readme.md b/ImageD11src/silxGui/readme.md → ImageD11/silxGui/readme.md
diff --git a/ImageD11src/silxGui/silx_colfile.py → ImageD11/silxGui/silx_colfile.py b/ImageD11src/silxGui/silx_colfile.py → ImageD11/silxGui/silx_colfile.py
diff --git a/ImageD11src/silxGui/silx_plot3d.py → ImageD11/silxGui/silx_plot3d.py b/ImageD11src/silxGui/silx_plot3d.py → ImageD11/silxGui/silx_plot3d.py
diff --git a/ImageD11src/silxGui/silx_sptview.py → ImageD11/silxGui/silx_sptview.py b/ImageD11src/silxGui/silx_sptview.py → ImageD11/silxGui/silx_sptview.py
diff --git a/ImageD11src/simplex.py → ImageD11/simplex.py b/ImageD11src/simplex.py → ImageD11/simplex.py
diff --git a/ImageD11src/sparseframe.py → ImageD11/sparseframe.py b/ImageD11src/sparseframe.py → ImageD11/sparseframe.py
diff --git a/ImageD11src/sym_u.py → ImageD11/sym_u.py b/ImageD11src/sym_u.py → ImageD11/sym_u.py
diff --git a/ImageD11src/symops.py → ImageD11/symops.py b/ImageD11src/symops.py → ImageD11/symops.py
diff --git a/ImageD11src/threshold_image.py → ImageD11/threshold_image.py b/ImageD11src/threshold_image.py → ImageD11/threshold_image.py
diff --git a/ImageD11src/tkGui/__init__.py → ImageD11/tkGui/__init__.py b/ImageD11src/tkGui/__init__.py → ImageD11/tkGui/__init__.py
diff --git a/ImageD11src/tkGui/guiindexer.py → ImageD11/tkGui/guiindexer.py b/ImageD11src/tkGui/guiindexer.py → ImageD11/tkGui/guiindexer.py
diff --git a/ImageD11src/tkGui/guimaker.py → ImageD11/tkGui/guimaker.py b/ImageD11src/tkGui/guimaker.py → ImageD11/tkGui/guimaker.py
diff --git a/ImageD11src/tkGui/guipeaksearch.py → ImageD11/tkGui/guipeaksearch.py b/ImageD11src/tkGui/guipeaksearch.py → ImageD11/tkGui/guipeaksearch.py
diff --git a/ImageD11src/tkGui/guisolver.py → ImageD11/tkGui/guisolver.py b/ImageD11src/tkGui/guisolver.py → ImageD11/tkGui/guisolver.py
diff --git a/ImageD11src/tkGui/guitransformer.py → ImageD11/tkGui/guitransformer.py b/ImageD11src/tkGui/guitransformer.py → ImageD11/tkGui/guitransformer.py
diff --git a/ImageD11src/tkGui/listdialog.py → ImageD11/tkGui/listdialog.py b/ImageD11src/tkGui/listdialog.py → ImageD11/tkGui/listdialog.py
diff --git a/ImageD11src/tkGui/plot3d.py → ImageD11/tkGui/plot3d.py b/ImageD11src/tkGui/plot3d.py → ImageD11/tkGui/plot3d.py
diff --git a/ImageD11src/tkGui/twodplot.py → ImageD11/tkGui/twodplot.py b/ImageD11src/tkGui/twodplot.py → ImageD11/tkGui/twodplot.py
@@ -337,27 +337,14 @@ def on_up(self,event):
 
 
 if __name__=="__main__":
-    import epffile, powbase, mcadata, ciidata
-    if len(sys.argv)<3:
-        import numpy as np
-        from math import pi
-        print("Usage: %s filename format"%(sys.argv[0]))
-        x=np.arange(0.0,3.0,0.01)
-        dat=epffile.powderdata(x,
-                               np.sin(2*pi*x)+5,
-                               np.sqrt(sin(2*pi*x)+5),
-                               { "title":"sin x" })
-    else:
-        try:
-            if sys.argv[2]=="powbase":
-                dat=powbase.powbase(sys.argv[1])
-            if sys.argv[2]=="epf":
-                dat=epffile.epffile(sys.argv[1])
-            if sys.argv[2]=="mca":
-                dat=mcadata.mcadata(sys.argv[1])
-        except:
-            print("Could not read your file %s" % (sys.argv[1]))
-            raise
+
+    import numpy as np
+    from math import pi
+    x=np.arange(0.0,3.0,0.01)
+    dat=epffile.powderdata(x,
+                           np.sin(2*pi*x)+5,
+                           np.sqrt(sin(2*pi*x)+5),
+                           { "title":"sin x" })
 
     root = Tk.Tk()
     root.wm_title("Two dimensional plotting")

diff --git a/ImageD11src/transform.py → ImageD11/transform.py b/ImageD11src/transform.py → ImageD11/transform.py
diff --git a/ImageD11src/transformer.py → ImageD11/transformer.py b/ImageD11src/transformer.py → ImageD11/transformer.py
diff --git a/ImageD11src/unitcell.py → ImageD11/unitcell.py b/ImageD11src/unitcell.py → ImageD11/unitcell.py
diff --git a/ImageD11src/weighted_kde.py → ImageD11/weighted_kde.py b/ImageD11src/weighted_kde.py → ImageD11/weighted_kde.py
diff --git a/ImageD11src/write_graindex_gv.py → ImageD11/write_graindex_gv.py b/ImageD11src/write_graindex_gv.py → ImageD11/write_graindex_gv.py
diff --git a/README.md b/README.md
@@ -6,9 +6,15 @@ Version 1.9.8, Jon Wright, [email protected]
 
 This is the source code for ImageD11. Probably you wanted a compiled version.
 
-You can try to get it via:
-
- `pip install ImageD11`
+If your pip is up-to-date, you can try to install it like this (numpy is needed
+to compile):
+```
+ python -m pip install --upgrade pip setuptools
+ python -m pip install numpy
+ python -m pip install ImageD11
+```
+To get all the possible dependencies too, you can try:
+ `python -m pip install ImageD11[full]`
 
 Some (dated) documentation is here: https://imaged11.readthedocs.io/
 
@@ -17,15 +23,15 @@ If you are at ESRF on an old linux computer you can try "module load fable".
 To use from git, try this:
 
  - Download and install python 3.7+, perhaps from www.python.org but probably from conda.
- - Preload packages from conda (or your system package manager): numpy, scipy, matplotlib, h5py, pillow, pycifrw, xfab
+ - Preload binary packages from conda (or your system package manager): 
+    numpy, scipy, matplotlib, h5py, pillow, pycifrw, xfab, pyqt, pillow, silx[full] etc
  - `pip install git+https://github.com/FABLE-3DXRD/ImageD11.git`
 
-If you want the sources then checkout like this:
+If you want to work with the sources then you can try like this:
  ```
+ $ python -m pip install --upgrade pip
  $ git clone https://github.com/FABLE-3DXRD/ImageD11.git && cd ImageD11
- $ python setup.py build bdist_wheel
- Followed by installation in your virtual or conda environment:
- $ pip install dist/ImageD11_[version you built].whl
+ $ python -m pip install --editable .
  ```
 
 After it is installed, you should find a script ImageD11_gui.py, somewhere in your path.

diff --git a/appveyor.yml b/appveyor.yml
@@ -15,12 +15,11 @@ install:
   - "SET PATH=%CONDA%;%CONDA%\\Scripts;%CONDA%\\Library\\bin;%CONDA%\\DLLS;%PATH%"
   - conda config --set always_yes yes --set changeps1 no
   - conda info -a
-  - python -m pip install --upgrade pip
-  - python -m pip install numpy h5py==2.10.0 --only-binary=h5py
-  - python setup.py build
-  - python -m pip install --ignore-installed certifi --upgrade-strategy only-if-needed --only-binary=h5py .
+  - python -m pip install --upgrade pip setuptools
+  - python -m pip install pytest numpy
+  - python -m pip install --ignore-installed certifi --upgrade-strategy only-if-needed --only-binary=h5py --editable .
 
 
 test_script:
-  - cd test
-  - python run_tests.py
+  - python -m pytest
+
diff --git a/sandbox/art.py b/sandbox/art.py
@@ -91,7 +91,8 @@ def update_wtd( recon, proj, angle, msk, dbg=True ):
 
 
 def make_data():
-    import rad, Image
+    import rad
+    from PIL import Image
     im = Image.open("phantom3.gif")
     a = np.asarray(im).astype(np.float32)
     print(a.min(),a.max())

diff --git a/sandbox/bgfilter_grab.py b/sandbox/bgfilter_grab.py
@@ -1,4 +1,6 @@
 
+
+from __future__ import print_function
 #import multiprocessing, os
 #cpu = str(multiprocessing.cpu_count())-1
 #os.environ['OPENBLAS_NUM_THREADS']=cpu

diff --git a/sandbox/ev78/integrate_them.py b/sandbox/ev78/integrate_them.py
@@ -1,5 +1,5 @@
 #!/usr/bin/python 
-
+from __future__ import print_function
 import sys
 #sys.path.append('/users/wright/software/lib/python')
 

diff --git a/sandbox/ev78/makevols.py b/sandbox/ev78/makevols.py
@@ -1,4 +1,6 @@
 
+from __future__ import print_function
+
 import fabio, numpy as np, h5py
 
 # read in .txt file and .dat files

diff --git a/sandbox/ev78/watch_direcs.py b/sandbox/ev78/watch_direcs.py
@@ -1,4 +1,5 @@
 
+from __future__ import print_function
 
 import glob, os, sys, time
 

diff --git a/sandbox/fit_rotating.py b/sandbox/fit_rotating.py
@@ -1,4 +1,6 @@
 
+from __future__ import print_function
+
 from scipy.spatial.transform import Rotation, RotationSpline
 from ImageD11 import grain, columnfile, cImageD11, transform
 import sys, numpy as np, pylab as pl, os

diff --git a/sandbox/indexer.py b/sandbox/indexer.py
@@ -19,8 +19,7 @@
 
 
 import numpy as np
-from ImageD11 import cImageD11, grain, transform
-import unitcell
+from ImageD11 import cImageD11, grain, transform, unitcell
 
 import math, time, sys, logging
 

diff --git a/sandbox/map/gridgrain.py b/sandbox/map/gridgrain.py
@@ -4,7 +4,7 @@
 
 #
 from ImageD11 import transform, transformer, indexing, parameters
-from ImageD11.closest import score
+from ImageD11.cImageD11 import score
 import sys
 
 

diff --git a/sandbox/map/gridmap.py b/sandbox/map/gridmap.py
@@ -4,7 +4,7 @@
 
 #
 from ImageD11 import transform, transformer, indexing, parameters
-from ImageD11.closest import score
+from ImageD11.cImageD11 import score
 import sys
 
 

diff --git a/sandbox/newpeaksearch.py b/sandbox/newpeaksearch.py
@@ -1,4 +1,5 @@
 
+from __future__ import print_function
 import sys
 import h5py, timeit
 import numpy as np

diff --git a/sandbox/offset_image.py b/sandbox/offset_image.py
@@ -2,6 +2,7 @@
 from __future__ import print_function
 
 import numpy as np
+from PIL import Image
 REAL = np.float 
 
 def normalise( im ):
@@ -39,7 +40,6 @@ def find_offset( c ):
 
 def register_image( rname, cname ):
     """ We take the current and place it onto reference """
-    import Image
     ref = normalise(np.asarray(Image.open(rname)).sum(axis=2, dtype=REAL))
     cur = normalise(np.asarray(Image.open(cname)).sum(axis=2, dtype=REAL))
     fftshape = ( ref.shape[0] + cur.shape[0] + 4,
@@ -77,7 +77,6 @@ def display_registered( current, reference, xf, yf ):
 
 
 def test(filename):
-    import Image
     rgb = np.asarray(Image.open(filename))
     vals = 1.0*rgb[:,:,0] + rgb[:,:,1] + rgb[:,:,2]
     print(vals.shape)

diff --git a/sandbox/segment.py b/sandbox/segment.py
@@ -1,4 +1,6 @@
 
+from __future__ import print_function
+
 import sys, timeit
 import numpy as np #, numba
 import scipy.ndimage 

diff --git a/sandbox/segment2d.py b/sandbox/segment2d.py
@@ -1,4 +1,5 @@
 
+from __future__ import print_function
 import sys, timeit
 import numpy as np #, numba
 import scipy.ndimage 

diff --git a/sandbox/segment_hdf_slurm/segment1.py b/sandbox/segment_hdf_slurm/segment1.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 
+from __future__ import print_function
 import os, time
 os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
 import h5py, hdf5plugin

diff --git a/setup.cfg b/setup.cfg
@@ -1,2 +1,2 @@
 [tool:pytest]
-norecursedirs = ImageD11src/depreciated
+norecursedirs = ImageD11/depreciated
Original file line number	Diff line number	Diff line change
		@@ -1,4 +1,5 @@

		from __future__ import print_function

		import glob, os, sys, time

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