Documentation

.travis.yml

@@ -47,11 +47,11 @@ install:
     - mkdir dev_tmp
     - cd dev_tmp
     # xtensor
-    - wget https://github.com/davidbrochart/xtensor/archive/fix_resize.tar.gz -O xtensor.tar.gz -q
+    - wget https://github.com/xtensor-stack/xtensor/archive/master.tar.gz -O xtensor.tar.gz -q
     - mkdir xtensor
     - tar zxf xtensor.tar.gz -C xtensor --strip-components 1
     # xtensor-io
-    - wget https://github.com/davidbrochart/xtensor-io/archive/io_config.tar.gz -O xtensor-io.tar.gz -q
+    - wget https://github.com/xtensor-stack/xtensor-io/archive/master.tar.gz -O xtensor-io.tar.gz -q
     - mkdir xtensor-io
     - tar zxf xtensor-io.tar.gz -C xtensor-io --strip-components 1
     # xtl

README.md

@@ -1,7 +1,142 @@
 # xtensor-zarr
 
 [![Travis](https://travis-ci.org/xtensor-stack/xtensor-zarr.svg?branch=master)](https://travis-ci.org/xtensor-stack/xtensor-zarr)
-[![Join the Gitter Chat](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/QuantStack/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![ReadTheDocs](https://readthedocs.org/projects/xtensor-zarr/badge/?version=stable)](http://xtensor-zarr.readthedocs.io/en/stable/)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davidbrochart/xtensor-zarr/zarr_v3?filepath=examples%2Fintroduction.ipynb)
+[![Join the Gitter Chat](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/QuantStack/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 Implementation of the Zarr version 3.0 core protocol based on xtensor
+
+## Introduction
+
+**xtensor-zarr is an early developer preview, and is not suitable for general usage yet. Features and implementation are subject to change.**
+
+`xtensor-zarr` offers an API to create and access a Zarr (v3) hierarchy in a store (locally or in the cloud), read and write arrays (in various formats) and groups in the hierarchy, and explore the hierarchy.
+
+## Installation
+
+`xtensor-zarr` is a header-only library. We provide a package for the conda package manager.
+
+```bash
+conda install xtensor-zarr -c conda-forge
+```
+
+- `xtensor-zarr` depends on `xtensor` `^0.21.9`, `xtensor` `^0.8` and `nlohmann_json`.
+
+- `google-cloud-cpp`, `cpp-filesystem`, `zlib`, and `blosc` are optional dependencies to `xtensor-zarr`.
+
+  - `google-cloud-cpp` is required to access a store in Google Cloud Storage.
+  - `cpp-filesystem` is required to access a store on the local file system.
+  - `zlib` is required for the GZip compressor.
+  - `blosc` is required for the Blosc compressor.
+
+All four libraries are available for the conda package manager.
+
+You can also install `xtensor-zarr` from source:
+
+```
+mkdir build
+cd build
+cmake ..
+make
+sudo make install
+```
+
+## Trying it online
+
+To try out xtensor-zarr interactively in your web browser, just click on the binder
+link:
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/davidbrochart/xtensor-zarr/zarr_v3?filepath=examples%2Fintroduction.ipynb)
+
+## Documentation
+
+To get started with using `xtensor-zarr`, check out the full documentation:
+
+http://xtensor-zarr.readthedocs.io/
+
+## Usage
+
+```cpp
+// create a hierarchy on the local file system
+xt::xzarr_file_system_store store("test.zr3");
+auto h = xt::create_zarr_hierarchy(store);
+
+// create an array in the hierarchy
+nlohmann::json attrs = {{"question", "life"}, {"answer", 42}};
+using S = std::vector<std::size_t>;
+S shape = {4, 4};
+S chunk_shape = {2, 2};
+xt::zarray a = h.create_array(
+    "/arthur/dent",  // path to the array in the store
+    shape,  // array shape
+    chunk_shape,  // chunk shape
+    "<f8",  // data type, here little-endian 64-bit floating point
+    'C',  // memory layout
+    '/',  // chunk identifier separator
+    xt::xio_binary_config(),  // compressor (here, raw binary)
+    attrs,  // attributes
+    10,  // chunk pool size
+    0.  // fill value
+);
+
+// write array data
+a(2, 1) = 3.;
+
+// read array data
+std::cout << a(2, 1) << std::endl;
+// prints `3.`
+std::cout << a(2, 2) << std::endl;
+// prints `0.` (fill value)
+std::cout << a.attrs() << std::endl;
+// prints `{"answer":42,"question":"life"}`
+
+// create a group
+auto g = h.create_group("/tricia/mcmillan", attrs);
+
+// explore the hierarchy
+// get children at a point in the hierarchy
+std::string children = h.get_children("/").dump();
+std::cout << children << std::endl;
+// prints `{"arthur":"implicit_group","marvin":"explicit_group","tricia":"implicit_group"}`
+// view the whole hierarchy
+std::string nodes = h.get_nodes().dump();
+std::cout << nodes << std::endl;
+// prints `{"arthur":"implicit_group","arthur/dent":"array","tricia":"implicit_group","tricia/mcmillan":"explicit_group"}`
+
+// use cloud storage
+// create an anonymous Google Cloud Storage client
+gcs::Client client((gcs::ClientOptions(gcs::oauth2::CreateAnonymousCredentials())));
+xzarr_gcs_store s1("zarr-demo/v3/test.zr3", client);
+// list keys under prefix
+auto keys1 = s1.list_prefix("data/root/arthur/dent/");
+for (const auto& key: keys1)
+{
+    std::cout << key << std::endl;
+}
+// prints:
+// data/root/arthur/dent/c0/0
+// data/root/arthur/dent/c0/1
+// data/root/arthur/dent/c1/0
+// data/root/arthur/dent/c1/1
+// data/root/arthur/dent/c2/0
+// data/root/arthur/dent/c2/1
+
+xzarr_gcs_store s2("zarr-demo/v3/test.zr3/meta/root/marvin", client);
+// list all keys
+auto keys2 = s2.list();
+for (const auto& key: keys2)
+{
+    std::cout << key << std::endl;
+}
+// prints:
+// android.array.json
+// paranoid.group.json
+```
+
+## License
+
+We use a shared copyright model that enables all contributors to maintain the
+copyright on their contributions.
+
+This software is licensed under the BSD-3-Clause license. See the [LICENSE](LICENSE) file for details.

docs/Doxyfile

@@ -0,0 +1,12 @@
+PROJECT_NAME      = "xtensor-zarr"
+XML_OUTPUT        = xml
+INPUT             = ../include
+GENERATE_LATEX    = NO
+GENERATE_MAN      = NO
+GENERATE_RTF      = NO
+CASE_SENSE_NAMES  = NO
+GENERATE_HTML     = NO
+GENERATE_XML      = YES
+RECURSIVE         = YES
+QUIET             = YES
+JAVADOC_AUTOBRIEF = YES

docs/Makefile

@@ -0,0 +1,187 @@
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext api
+
+default: html
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  applehelp  to make an Apple Help Book"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+	rm -rf xml
+
+html:
+	doxygen
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	doxygen
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	doxygen
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	doxygen
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	doxygen
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	doxygen
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+epub:
+	doxygen
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	doxygen
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	doxygen
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	doxygen
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	doxygen
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	doxygen
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	doxygen
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	doxygen
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	doxygen
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	doxygen
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	doxygen
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	doxygen
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+coverage:
+	doxygen
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
+
+xml:
+	doxygen
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	doxygen
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/environment.yml

@@ -0,0 +1,7 @@
+name: xtensor-zarr-docs
+
+channels:
+  - conda-forge
+
+dependencies:
+  - breathe