MAINT: Fix codecov jobs and update pre-commit

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Chris Holdgraf <choldgraf@gmail.com>
Co-authored-by: Chris Holdgraf <choldgraf@berkeley.edu>

Author: pre-commit-ci[bot]

.github/workflows/tests.yml

@@ -62,7 +62,7 @@ jobs:
       # this is why we run `coverage xml` afterwards (required by codecov)
 
     - name: Upload to Codecov
-      if: github.repository == 'executablebooks/MyST-NB'
+      if: github.repository == 'executablebooks/MyST-NB' && matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'
       uses: codecov/codecov-action@v1
       with:
         name: myst-nb-pytests

.pre-commit-config.yaml

@@ -12,37 +12,37 @@ exclude: >
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
     - id: check-json
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.2
+    rev: v3.3.1
     hooks:
     - id: pyupgrade
       args: [--py37-plus]
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
     - id: isort
 
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.3.0
     hooks:
     - id: black
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+    rev: 6.0.0
     hooks:
     - id: flake8
       additional_dependencies: [flake8-bugbear]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.990
+    rev: v1.2.0
     hooks:
     - id: mypy
       args: [--config-file=pyproject.toml]

docs/authoring/jupyter-notebooks.md

@@ -16,7 +16,7 @@ Sphinx using the MyST parser.[^download]
 
 :::{seealso}
 For more information about what you can write with MyST Markdown, see the
-[MyST Parser syntax guide](myst:syntax/syntax).
+[MyST Parser documentation](myst:intro/get-started).
 :::
 
 ### Configuration

docs/conf.py

@@ -177,7 +177,6 @@ def field_type(field):
             return ctype
 
     class MystNbConfigDirective(_ConfigBase):
-
         required_arguments = 1
         option_spec = {
             "sphinx": directives.flag,
@@ -197,7 +196,6 @@ def run(self):
             text = self.table_header()
             count = 0
             for name, value, field in config.as_triple():
-
                 # filter by sphinx options
                 if "sphinx" in self.options and field.metadata.get("sphinx_exclude"):
                     continue
@@ -239,7 +237,6 @@ def run(self):
             return node.children
 
     class MystConfigDirective(_ConfigBase):
-
         option_spec = {
             "sphinx": directives.flag,
         }
@@ -250,7 +247,6 @@ def run(self):
             text = self.table_header()
             count = 0
             for name, value, field in config.as_triple():
-
                 # filter by sphinx options
                 if "sphinx" in self.options and field.metadata.get("sphinx_exclude"):
                     continue

myst_nb/core/execute/inline.py

@@ -34,7 +34,6 @@ class NotebookClientInline(NotebookClientBase):
     """
 
     def start_client(self):
-
         self._tmp_path = None
         if self.nb_config.execution_in_temp:
             self._tmp_path = mkdtemp()
@@ -114,12 +113,10 @@ def close_client(self, exc_type, exc_val, exc_tb):
     def code_cell_outputs(
         self, cell_index: int
     ) -> tuple[int | None, list[NotebookNode]]:
-
         cells = self.notebook.get("cells", [])
 
         # ensure all cells up to and including the requested cell have been executed
         while (not self._cell_error) and cell_index > self._last_cell_executed:
-
             self._last_cell_executed += 1
             try:
                 next_cell = cells[self._last_cell_executed]

myst_nb/core/nb_to_tokens.py

@@ -37,7 +37,6 @@ def notebook_to_tokens(
     # (required to collect all reference definitions, before assessing references).
     block_tokens = [Token("nb_initialise", "", 0, map=[0, 0])]
     for cell_index, nb_cell in enumerate(notebook.cells):
-
         # skip empty cells
         if len(nb_cell["source"].strip()) == 0:
             continue

myst_nb/core/read.py

@@ -242,7 +242,6 @@ def _flush_markdown(start_line, token, md_metadata):
     md_metadata: dict = {}
 
     for token in tokens:
-
         nesting_level += token.nesting
 
         if nesting_level != 0:

myst_nb/core/render.py

@@ -192,7 +192,6 @@ def render_nb_cell_code(self: SelfType, token: SyntaxTreeNode) -> None:
 
         self.add_line_and_source_path(cell_container, token)
         with self.current_node_context(cell_container, append=True):
-
             # render the code source code
             if not remove_input:
                 cell_input = nodes.container(

myst_nb/docutils_.py

@@ -301,7 +301,6 @@ def _render_nb_cell_code_outputs(
                 self.add_line_and_source_path_r(_nodes, token)
                 self.current_node.extend(_nodes)
             elif output.output_type in ("display_data", "execute_result"):
-
                 # Note, this is different to the sphinx implementation,
                 # here we directly select a single output, based on the mime_priority,
                 # as opposed to output all mime types, and select in a post-transform

myst_nb/ext/glue/roles.py

@@ -29,7 +29,6 @@ class PasteRoleAny(RoleBase):
     """
 
     def run(self) -> tuple[list[nodes.Node], list[nodes.system_message]]:
-
         # check if this is a pending reference
         doc_key = self.text.split("::", 1)
         if len(doc_key) == 2: