Merge pull request #985 from minrk/rm-stencila

Drop support for stencila

Author: betatim

.github/workflows/test.yml

@@ -74,7 +74,6 @@ jobs:
           - nix
           - pipfile
           - r
-          - stencila-py
           - unit
           - venv
         include:

docs/source/architecture.md

@@ -44,10 +44,9 @@ It takes the following steps to determine this:
    repository' by returning `True`. Usually buildpacks look for presence of specific files
    (`requirements.txt`, `environment.yml`, `install.R`, `manifest.xml` etc) to determine if they can handle a
    repository or not. Buildpacks may also look into specific files to determine specifics of the
-   required environment, such as the Stencila integration which extracts the required language-specific
-   executions contexts from an XML file (see base `BuildPack`). More than one buildpack may use such
-   information, as properties can be inherited (e.g. the R buildpack uses the list of required Stencila
-   contexts to see if R must be installed).
+   required environment.
+   More than one buildpack may use such information,
+   as properties can be inherited.
 3. If no `BuildPack` returns true, then repo2docker will use the default `BuildPack` (defined in
    `Repo2Docker.default_buildpack` traitlet).
 

docs/source/config_files.rst

@@ -149,25 +149,6 @@ You also need to have a ``runtime.txt`` file that is formatted as
 used for your R installation.
 
 
-.. _manifest.xml:
-
-``manifest.xml`` - Install Stencila
-===================================
-
-`Stencila <https://stenci.la/>`_ is an open source office suite for reproducible research.
-It is powered by the open file format `Dar <https://github.com/substance/dar>`_.
-
-If your repository contains a Stencila document, repo2docker detects it based on the file ``manifest.xml``.
-The required `execution contexts <https://stenci.la/learn/intro.html>`_ are extracted from a Dar article (i.e.
-files named ``*.jats.xml``).
-
-You may also have a ``runtime.txt`` and/or an ``install.R`` to manually configure your R installation.
-
-To see example repositories, visit our
-`Stencila with R <https://github.com/binder-examples/stencila-r/>`_ and
-`Stencila with Python <https://github.com/binder-examples/stencila-py>`_ examples.
-
-
 .. _postBuild:
 
 ``postBuild`` - Run code after installing the environment

docs/source/howto/user_interface.rst

@@ -112,18 +112,7 @@ http://mybinder.org/v2/gh/binder-examples/r/master?urlpath=shiny/bus-dashboard/
 Stencila
 ========
 
-The Stencila user interface is automatically enabled if a Stencila document (i.e.
-a file ``manifest.xml``) is detected. Stencila will be accessible by appending
-``/stencila`` to the URL, like so:
+.. note::
 
-.. code-block:: none
-
-   http(s)://<server:port>/stencila
-
-The editor will open the Stencila document corresponding to the last ``manifest.xml``
-found in the file tree. If you want to open a different document, you can configure
-the path in the URL parameter ``archive``:
-
-.. code-block:: none
-
-   http(s)://<server:port>/stencila/?archive=other-dir
+   Stencila support has been removed due to changes in stencila making it incompatible.
+   Please `get in touch <https://discourse.jupyter.org>`__ if you would like to help restore stencila support.

repo2docker/buildpacks/base.py

@@ -311,70 +311,16 @@ def get_build_script_files(self):
         """
         return {}
 
-    @property
-    def stencila_manifest_dir(self):
-        """Find the stencila manifest dir if it exists"""
-        if hasattr(self, "_stencila_manifest_dir"):
-            return self._stencila_manifest_dir
-
-        # look for a manifest.xml that suggests stencila could be used
-        # when we find one, stencila should be installed
-        # and set environment variables such that
-        # this file is located at:
-        # ${STENCILA_ARCHIVE_DIR}/${STENCILA_ARCHIVE}/manifest.xml
-
-        self._stencila_manifest_dir = None
+    def _check_stencila(self):
+        """Find the stencila manifest dir if it exists
 
+        And warn about removed stencila support
+        """
         for root, dirs, files in os.walk("."):
             if "manifest.xml" in files:
-                self.log.debug("Found a manifest.xml at %s", root)
-                self._stencila_manifest_dir = root.split(os.path.sep, 1)[1]
-                self.log.info(
-                    "Using stencila manifest.xml in %s", self._stencila_manifest_dir
+                self.log.error(
+                    f"Found a stencila manifest.xml at {root}. Stencila is no longer supported."
                 )
-                break
-        return self._stencila_manifest_dir
-
-    @property
-    def stencila_contexts(self):
-        """Find the stencila manifest contexts from file path in manifest"""
-        if hasattr(self, "_stencila_contexts"):
-            return self._stencila_contexts
-
-        # look at the content of the documents in the manifest
-        # to extract the required execution contexts
-        self._stencila_contexts = set()
-
-        # get paths to the article files from manifest
-        files = []
-        if self.stencila_manifest_dir:
-            manifest = ET.parse(
-                os.path.join(self.stencila_manifest_dir, "manifest.xml")
-            )
-            documents = manifest.findall("./documents/document")
-            files = [
-                os.path.join(self.stencila_manifest_dir, x.get("path"))
-                for x in documents
-            ]
-
-        else:
-            return self._stencila_contexts
-
-        for filename in files:
-            self.log.debug("Extracting contexts from %s", filename)
-
-            # extract code languages from file
-            document = ET.parse(filename)
-            code_chunks = document.findall('.//code[@specific-use="source"]')
-            languages = [x.get("language") for x in code_chunks]
-            self._stencila_contexts.update(languages)
-
-            self.log.info(
-                "Added executions contexts, now have %s", self._stencila_contexts
-            )
-            break
-
-        return self._stencila_contexts
 
     def get_build_scripts(self):
         """
@@ -553,6 +499,9 @@ def render(self, build_args=None):
             for k, v in self.get_build_script_files().items()
         }
 
+        # check if there's a stencila manifest, support for which has been removd
+        self._check_stencila()
+
         return t.render(
             packages=sorted(self.get_packages()),
             path=self.get_path(),
@@ -706,23 +655,7 @@ def get_build_scripts(self):
 
     def get_env(self):
         """Return env directives to be set after build"""
-        env = []
-        if self.stencila_manifest_dir:
-            # manifest_dir is the path containing the manifest.xml
-            # archive_dir is the directory containing archive directories
-            # (one level up) default archive is the name of the directory
-            # in the archive_dir such that
-            # ${STENCILA_ARCHIVE_DIR}/${STENCILA_ARCHIVE}/manifest.xml
-            # exists.
-
-            archive_dir, archive = os.path.split(self.stencila_manifest_dir)
-            env.extend(
-                [
-                    ("STENCILA_ARCHIVE_DIR", "${REPO_DIR}/" + archive_dir),
-                    ("STENCILA_ARCHIVE", archive),
-                ]
-            )
-        return env
+        return []
 
     def detect(self):
         return True
@@ -765,32 +698,6 @@ def get_preassemble_scripts(self):
         except FileNotFoundError:
             pass
 
-        if "py" in self.stencila_contexts:
-            scripts.extend(
-                [
-                    (
-                        "${NB_USER}",
-                        r"""
-                        ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache https://github.com/stencila/py/archive/f1260796.tar.gz && \
-                        ${KERNEL_PYTHON_PREFIX}/bin/python -m stencila register
-                        """,
-                    )
-                ]
-            )
-        if self.stencila_manifest_dir:
-            scripts.extend(
-                [
-                    (
-                        "${NB_USER}",
-                        r"""
-                        ${NB_PYTHON_PREFIX}/bin/pip install --no-cache nbstencilaproxy==0.1.1 && \
-                        jupyter serverextension enable --sys-prefix --py nbstencilaproxy && \
-                        jupyter nbextension install    --sys-prefix --py nbstencilaproxy && \
-                        jupyter nbextension enable     --sys-prefix --py nbstencilaproxy
-                        """,
-                    )
-                ]
-            )
         return scripts
 
     def get_assemble_scripts(self):

repo2docker/buildpacks/r.py

@@ -25,8 +25,6 @@ class RBuildPack(PythonBuildPack):
 
     2. A `DESCRIPTION` file signaling an R package
 
-    3. A Stencila document (*.jats.xml) with R code chunks (i.e. language="r")
-
     If there is no `runtime.txt`, then the MRAN snapshot is set to latest
     date that is guaranteed to exist across timezones.
 
@@ -37,8 +35,7 @@ class RBuildPack(PythonBuildPack):
 
     - as dependencies in a `DESCRIPTION` file
 
-    - are needed by a specific tool, for example the package `stencila` is
-      installed and configured if a Stencila document is given.
+    - are needed by a specific tool
 
     The `r-base` package from Ubuntu apt repositories is used to install
     R itself, rather than any of the methods from https://cran.r-project.org/.
@@ -129,9 +126,7 @@ def detect(self):
             return True
 
         description_R = "DESCRIPTION"
-        if (
-            not self.binder_dir and os.path.exists(description_R)
-        ) or "r" in self.stencila_contexts:
+        if not self.binder_dir and os.path.exists(description_R):
             if not self.checkpoint_date:
                 # no R snapshot date set through runtime.txt
                 # set the R runtime to the latest date that is guaranteed to
@@ -226,7 +221,6 @@ def get_build_scripts(self):
           (determined by MRAN)
         - IRKernel
         - nbrsessionproxy (to access RStudio via Jupyter Notebook)
-        - stencila R package (if Stencila document with R code chunks detected)
 
         We set the snapshot date used to install R libraries from based on the
         contents of runtime.txt.
@@ -325,34 +319,6 @@ def get_build_scripts(self):
             ),
         ]
 
-        if "r" in self.stencila_contexts:
-            # new versions of R require a different way of installing bioconductor
-            if V(self.r_version) <= V("3.5"):
-                scripts += [
-                    (
-                        "${NB_USER}",
-                        # Install and register stencila library
-                        r"""
-                    R --quiet -e "source('https://bioconductor.org/biocLite.R'); biocLite('graph')" && \
-                    R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \
-                    R --quiet -e "stencila::register()"
-                    """,
-                    )
-                ]
-
-            else:
-                scripts += [
-                    (
-                        "${NB_USER}",
-                        # Install and register stencila library
-                        r"""
-                    R --quiet -e "install.packages('BiocManager'); BiocManager::install(); BiocManager::install(c('graph'))" && \
-                    R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \
-                    R --quiet -e "stencila::register()"
-                    """,
-                    )
-                ]
-
         return super().get_build_scripts() + scripts
 
     def get_preassemble_script_files(self):