updated package generation and added conda recipe

.appveyor.yml

@@ -10,8 +10,7 @@ environment:
 before_build:
   - cmd: set PATH=%CONDA%;%CONDA%\Scripts;%CONDA%\Library\bin;%CONDA%\Library\mingw-w64\bin;%PATH%
   - cmd: conda config --add channels conda-forge
-  - cmd: conda config --add channels bioconda
-  - cmd: conda config --add channels csachs
+  - cmd: conda config --add channels modsim
   - cmd: conda update -y conda
   # pyinstaller is currently not working in conjunction with mycelyso, hopefully a pinned commit will resolve this
   - cmd: pip install https://github.com/pyinstaller/pyinstaller/archive/15770dadce1227b6772aac68f08ad8eed3d13f99.zip

.dockerignore

@@ -0,0 +1,7 @@
+.git/
+local/
+dist/
+*.egg-info/
+docs/
+build/
+.idea/

.gitignore

@@ -3,6 +3,7 @@ docs/_build/
 .idea/
 build/
 dist/
+local/
 examples/*.tif
 examples/*.tiff
 *.egg-info/

Dockerfile

@@ -1,18 +1,21 @@
-FROM continuumio/miniconda3:4.7.10-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
+COPY . /tmp/package
 
-RUN conda config --add channels conda-forge --add channels bioconda --add channels csachs && \
-    conda install -y jupyter mycelyso mycelyso-inspector && \
-    pip uninstall -y mycelyso && \
-    wget https://github.com/modsim/mycelyso/archive/master.tar.gz -O - | tar zx -C /tmp && mv /tmp/mycelyso-master /tmp/package && \
-    pip install /tmp/package && \
+
+RUN \
+    wget https://github.com/modsim/mycelyso-inspector/archive/master.tar.gz -O - | tar zx -C /tmp && \
+    # conda build needs bash
+    apk add --no-cache bash git && \
+    conda install -c conda-forge conda-build conda-verify && \
+    conda build -c conda-forge -c modsim /tmp/mycelyso-inspector-master/recipe && \
+    conda build -c conda-forge -c modsim /tmp/package/recipe && \
+    conda install -c conda-forge -c modsim -c local -y python==3.7 jupyter mycelyso mycelyso-inspector && \
     mv /tmp/package/examples / && \
     rm -rf /tmp/package && \
     busybox adduser --disabled-password user && \
@@ -23,6 +26,7 @@ RUN conda config --add channels conda-forge --add channels bioconda --add channe
     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 && \ # keep the package in the Docker image
     echo Done
 
 USER user
@@ -31,4 +35,4 @@ WORKDIR /data
 
 EXPOSE 8888
 
-ENTRYPOINT ["python", "-m", "mycelyso"]
+ENTRYPOINT ["python", "-m", "mycelyso"]

README.rst

@@ -100,13 +100,12 @@ not be present in the PyPI (Python Package Index). Thankfully the conda Package
 provides all packages necessary in an easy to use manner. To use it, please `download Anaconda <https://www.continuum.io/downloads>`_ (Miniconda could be downloaded
 as well, but as most packages included in Anaconda are needed anyways, it does hardly provide a size benefit).
 
-You have to enable the necessary channels (we aim to add mycelyso to `bioconda <https://bioconda.github.io>`_ lateron):
+You have to enable the necessary channels:
 
 .. code-block:: bash
 
     > conda config --add channels conda-forge
-    > conda config --add channels bioconda
-    > conda config --add channels csachs
+    > conda config --add channels modsim
 
     > conda install -y mycelyso mycelyso-inspector
 

recipe/meta.yaml

@@ -0,0 +1,56 @@
+{% set name = "mycelyso" %}
+{% set version = "1.0.1.dev1" %}
+#{% set sha256 = "9804cdc22d88beb6f0e6e87870fe962d57aacd6415ba2a5b5ef3c1010cd7f5bf" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+#  fn: {{ name }}-{{ version }}.tar.gz
+#  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+#  sha256: {{ sha256 }}
+  path: ..
+
+build:
+  number: 0
+  script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv
+  noarch: python
+
+requirements:
+  build:
+    - python
+    - setuptools
+  run:
+    - numpy
+    - scipy
+    - matplotlib
+    - scikit-image
+    - networkx
+    - pytables
+    - numexpr
+    - pandas
+    - pilyso-io
+    - mfisp-boxdetection
+    - molyso
+    - tunable
+    - tqdm
+
+test:
+  imports:
+    - mycelyso
+
+about:
+  home: https://github.com/modsim/mycelyso
+  license: BSD-2-Clause
+  license_family: BSD
+  summary: 'mycelyso - MYCEelium anaLYsis SOftware'
+  description: |
+    MYCEelium anaLYsis SOftware, see https://github.com/modsim/mycelyso for details.
+
+  doc_url: https://mycelyso.readthedocs.io
+  dev_url: https://github.com/modsim/mycelyso
+
+extra:
+  recipe-maintainers:
+    - csachs