various cleanups, among others for better conda / Docker building

Author: csachs

Dockerfile

@@ -1,26 +1,24 @@
-FROM continuumio/miniconda3:4.7.12-alpine
+FROM continuumio/miniconda3:4.9.2-alpine
 LABEL maintainer=c.sachs@fz-juelich.de
 
 USER root
 
 ENV PATH "$PATH:/opt/conda/bin:/bin/sbin:/usr/bin"
 
-# we could copy the files from the current directory, but that would create an additional layer ...
 COPY . /tmp/package
 
 WORKDIR /tmp/package
 
 RUN \
     # conda build needs bash
     apk add --no-cache bash mesa-gl && \
-    conda config --add channels conda-forge --add channels bioconda --add channels csachs && \
-    conda install -y conda-build conda-verify && \
-    conda build recipe && \
-    conda install -c local -y molyso && \
-    conda install -y jupyter pandas && \
+    conda install -c conda-forge conda-build conda-verify && \
+    conda build -c conda-forge -c modsim /tmp/package/recipe && \
+    conda install -c conda-forge -c modsim -c local -y python=3.7 molyso jupyter pandas && \
     # missing libGL causes cv2 to fail in a very pecuilar way ... although it just throws an ImportError
     # molyso will randomly crash later when importing matplotlib.pyplot
-    cp -R  /tmp/package/examples /examples && \
+    mv /tmp/package/examples / && \
+    rm -rf /tmp/package && \
     busybox adduser --disabled-password user && \
     ln -s /examples /home/user && \
     mkdir /data && \
@@ -29,7 +27,7 @@ RUN \
     echo "c.NotebookApp.ip = '0.0.0.0'" >> /home/user/.jupyter/jupyter_notebook_config.py && \
     echo "c.NotebookApp.notebook_dir = '/home/user'" >> /home/user/.jupyter/jupyter_notebook_config.py && \
     conda clean -afy || true && \
-    conda build purge-all && \
+    # conda build purge-all && \ # keep the package in the Docker image
     echo Done
 
 USER user

README.rst

@@ -177,6 +177,7 @@ Example:
 
 
 Supported are among others: the acquisition :code:`interval` (seconds), and the pixel size :code:`calibration` in um per pixel.
+Some older files may have incorrectly labeled axes, since molyso expects the time axis to be correctly labeled, it might be necessary to reorder the axes, this can be done on the fly, by passing e.g. :code:`?swap_axes=Z..T`.
 Don't forget to escape/quote the ? in the command line.
 
 

recipe/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "molyso" %}
-{% set version = "1.0.5" %}
-{% set sha256 = "02f9cdf1986a848e35b46d6e2ad64cc98c536bdb6fcaf36da6a0902df8a8c1ad" %}
+{% set version = "1.0.6" %}
+#{% set sha256 = "02f9cdf1986a848e35b46d6e2ad64cc98c536bdb6fcaf36da6a0902df8a8c1ad" %}
 
 package:
   name: {{ name|lower }}
@@ -25,9 +25,7 @@ requirements:
     - numpy
     - scipy
     - matplotlib
-    - tifffile
-    - nd2file
-    - czifile
+    - pilyso-io
     - jsonpickle
     - tqdm
     - opencv

setup.py

@@ -28,10 +28,9 @@
         'License :: OSI Approved :: BSD License',
         'Operating System :: POSIX',
         'Operating System :: POSIX :: Linux',
-        'Operating System :: MacOS :: MacOS X',   # lately no tests
+        'Operating System :: MacOS :: MacOS X',
         'Operating System :: Microsoft :: Windows',
-        'Programming Language :: Python :: 3',    #
-        'Programming Language :: Python :: 3.5',  # main focus
+        'Programming Language :: Python :: 3',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
         'Topic :: Scientific/Engineering :: Image Recognition',
     ]