fgbossema · fgbossema · Jun 13, 2019 · Jun 13, 2019 · Jun 7, 2019 · Jun 13, 2019
diff --git a/.gitignore b/.gitignore
@@ -103,4 +103,6 @@ venv.bak/
 # mypy
 .mypy_cache/
 
-*~
+# IntellIJ
+.idea/
+*~
diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/Makefile b/Makefile
@@ -1,18 +1,65 @@
+.PHONY: clean clean-test clean-pyc clean-build docs help install_dev
+.DEFAULT_GOAL := help
 
-.PHONY: install docs
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
 
-install:
+try:
+	from urllib import pathname2url
+except:
+	from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+clean: clean-build clean-pyc
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+docs/.nojekyll:
+	touch docs/.nojekyll
+
+docs: docs/.nojekyll install_dev ## generate Sphinx HTML documentation, including API docs
+	make --directory doc_sources clean
+	make --directory doc_sources html
+	$(BROWSER) docs/index.html
+
+install: clean ## install the package to the active Python's site-packages
 	pip install .
 
-install_dev:
-	# https://stackoverflow.com/a/28842733
+install_dev: ## install in editable mode
 	pip install -e .[dev]
 
-docs: install_dev
-	@cd doc_sources && make html
-
-style: install_dev
-	black flexdata
+conda_package:  ## build Conda package
+	conda build conda/ -c astra-toolbox -c nvidia
 
-conda_package: install_dev
-	conda build conda/ -c astra-toolbox/label/dev -c conda-forge -c owlas
+pypi_wheels: ## build wheel package for PyPI
+	python -m build --wheel
diff --git a/README.md b/README.md
@@ -1,49 +1,42 @@
 # flexDATA
 
-This project is a part of the larger X-ray tomographic reconstruction toolbox comprised of [flexDATA], [flexTOMO] and [flexCALC].
-flexDATA contains IO routines that were originally developed for the Flex-Ray X-ray CT scanner but can be used for reading and writing data from other types of CT scanners. It provides an interface between a scanner and a GPU-based CT reconstruction [ASTRA toolbox](https://www.astra-toolbox.com/). It can be especially helpful when the scanner has many degrees of freedom and the geometry of each scan is defined by a large number of parameters.
+This project is a part of the larger X-ray tomographic reconstruction toolbox comprised of [flexDATA](https://github.com/cicwi/flexDATA), [flexTOMO](https://github.com/cicwi/flexTOMO) and [flexCALC](https://github.com/cicwi/flexCALC).
+flexDATA contains IO routines that were originally developed for the Flex-Ray X-ray CT scanner but can be used for reading and writing data from other types of CT scanners. It provides an interface between a scanner and a GPU-based CT reconstruction [ASTRA Toolbox](https://github.com/astra-toolbox/astra-toolbox). It can be especially helpful when the scanner has many degrees of freedom and the geometry of each scan is defined by a large number of parameters.
 
 ## Getting Started
 
-It takes a few steps to setup flexDATA on your machine. We recommend that the user installs [Anaconda package manager](https://www.anaconda.com/download/) for Python 3.
+It takes a few steps to setup flexDATA on your machine. We recommend that the user installs [conda package manager](https://docs.anaconda.com/miniconda/) for Python 3.
 
 ### Installing with conda
 
-Simply install with:
-```
-conda create -n <your-environment> python=3.6
-conda install -c cicwi -c astra-toolbox/label/dev -c conda-forge -c owlas flexdata
-```
+`conda install flexdata -c cicwi -c astra-toolbox -c nvidia`
 
-### Installing from source
+### Installing with pip
 
-To install flexDATA you will need the latest version of the ASTRA toobox (preferably development version). It can be installed via command line with Anaconda:
+`pip install flexdata`
 
-```
-conda install -c astra-toolbox/label/dev astra-toolbox
-```
+### Installing from source
 
-To install flexDATA, simply clone this GitHub project. Go to the cloned directory and run PIP installer:
-```
+```bash
 git clone https://github.com/cicwi/flexdata.git
 cd flexdata
 pip install -e .
 ```
 
 ## Running the examples
 
-To learn about the functionality of the package check out our examples folder. Examples are separated into blocks that are best to run in Spyder environment step-by-step.
+To learn about the functionality of the package check out our `examples/` folder. Examples are separated into blocks that are best to run in VS Code / Spyder environment step-by-step.
 
 ## Modules
 
 flexDATA is comprised of the following modules:
 
-* data:     read / write raw projection stacks (tiffs), parse settings file of the scanner to produce meta data.
-* geometry:  geometry classes (circular, helical and linear).
-* display: simple display routines for 3D arrays
+* `flexdata.data`: Read / write raw projection stacks (tiffs), parse settings file of the scanner to produce meta data.
+* `flexdata.geometry`: Geometry classes (circular, helical and linear).
+* `flexdata.display`: Simple display routines for 3D arrays
 
-Typical code:
-```
+Typical usage:
+```python
 # Import:
 from flexdata import data
 
@@ -52,7 +45,7 @@ proj = data.read_tiffs(path, file_name)
 flat = data.read_tiffs(path, file_name)
 
 # Read metadata:
-geom = data.read_flexraylog(path) 
+geom = data.read_flexraylog(path)
 
 # Generate an ASTRA-compatible projection geometry description:
 proj_geom = geom.astra_proj_geom(proj.shape)
@@ -63,19 +56,19 @@ proj_geom = geom.astra_proj_geom(proj.shape)
 * **Alexander Kostenko** - *Initial work*
 * **Allard Hendriksen** - *Packaging and installation*
 * **Jan-Willem Buurlage** - *Packaging and installation*
+* **Willem Jan Palenstijn** - *Packaging, installation and maintenance*
+* **Alexander Skorikov** - *Packaging, installation and maintenance*
 
 See also the list of [contributors](https://github.com/cicwi/flexdata/contributors) who participated in this project.
 
 ## How to contribute
 
-Contributions are always welcome. Please submit pull requests against the `develop` branch.
-
-If you have any issues, questions, or remarks, then please open an issue on GitHub.
+Contributions are always welcome. If you have any issues, questions, or remarks, then please open an issue on GitHub.
 
 ## License
 
 This project is licensed under the GNU GENERAL PUBLIC License - see the [LICENSE.md](LICENSE.md) file for details
 
 ## Acknowledgments
 
-* To Willem Jan Palenstijn for endles advices regarding the use of ASTRA toolbox.
+* To Willem Jan Palenstijn for endless advices regarding the use of ASTRA toolbox.
diff --git a/conda/build.sh b/conda/build.sh
diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -8,17 +8,19 @@ source:
     path: ../
 
 build:
-    number: '0'
+    noarch: python
+    number: 0
+    script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-build-isolation --verbose
 
 requirements:
-    build:
-        - python {{ python }}
-        - tifffile
-        - transforms3d
-        - pyqtgraph
+    host:
+        - python >=3.7
+        - pip
+        - setuptools
+        - wheel
 
     run:
-        - python
+        - python >=3.7
         # dependencies are defined in setup.py
         {% for dep in data['install_requires'] %}
         - {{ dep.lower() }}
@@ -28,7 +30,3 @@ about:
     home: https://github.com/cicwi/flexDATA
     license_file: LICENSE.md
     summary: "This project comprises IO routines for CT data."
-
-extra:
-    maintainers:
-        - Alexander Kostenko
diff --git a/doc_sources/LICENSE.md b/doc_sources/LICENSE.md
@@ -0,0 +1 @@
+../LICENSE.md
diff --git a/doc_sources/readme.md → doc_sources/README.md b/doc_sources/readme.md → doc_sources/README.md
diff --git a/doc_sources/changelog.md b/doc_sources/changelog.md
diff --git a/doc_sources/conf.py b/doc_sources/conf.py
@@ -22,14 +22,6 @@
 # sys.path.insert(0, os.path.abspath('.'))
 
 
-# -- Support markdown -----------------------------------------------------
-# See: <https://blog.readthedocs.com/adding-markdown-support/>
-
-from recommonmark.parser import CommonMarkParser
-source_parsers = {'.md': CommonMarkParser}
-source_suffix = ['.rst', '.md']
-
-
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -43,6 +35,7 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.todo',
     'sphinx.ext.viewcode',
+    'myst_parser'
 ]
 
 # Add any paths that contain templates here, relative to this directory.

diff --git a/doc_sources/index.rst b/doc_sources/index.rst
@@ -1,8 +1,3 @@
-.. flexdata documentation master file, created by
-   sphinx-quickstart on Wed Oct 24 14:50:47 2018.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 Welcome to flexdata's documentation!
 ====================================
 
@@ -12,9 +7,8 @@ Contents:
    :maxdepth: 2
 
 
-   readme
+   README.md
    flexdata
-   changelog
 
 
 Indices and tables

diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 29126bc7917be84467c57b79940f875c
+config: 52e211fcd5f58437c04148d4e19aab7f
 tags: 645f666f9bcd5a90fca523b33c5a78b7
-Original file line number
+Diff line change
@@ Expand Up / @@ -103,4 +103,6 @@ venv.bak/ @@
     # mypy
     .mypy_cache/
-    *~
+    # IntellIJ
+    .idea/
+    *~