mwouts · mwouts · Nov 23, 2023 · Nov 6, 2023 · Nov 6, 2023 · Nov 7, 2023
diff --git a/codecov.yml → .github/codecov.yml b/codecov.yml → .github/codecov.yml
@@ -1,21 +1,20 @@
 codecov:
-    notify:
-        after_n_builds: 11
+  notify:
+    after_n_builds: 11
 
 comment:
   after_n_builds: 11
 
 coverage:
   status:
     project:
-      default: false  # disable the default status that measures entire project
       tests:
         paths:
           - "tests/"
         target: 100%
       source:
         paths:
-          - "jupytext/"
+          - "src/jupytext/"
         target: 97%
         threshold: 0.002
     patch:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -13,7 +13,7 @@
 exclude: >
     (?x)^(
       demo/.*|
-      tests/notebooks/.*|
+      tests/data/notebooks/.*|
     )$
 repos:
 

diff --git a/docs/contributing.md b/docs/contributing.md
@@ -20,5 +20,5 @@ You want to submit an enhancement on Jupytext? Unless this is a small change, we
 A pull request for which you do not need to contact us in advance is the addition of a new language to Jupytext. In principle that should be easy - you would only have to:
 - document the language extension and comment by adding one line to `_SCRIPT_EXTENSIONS` in `jupytext/languages.py`.
 - add the language to `docs/languages.md`
-- contribute a sample notebook in `tests/notebooks/ipynb_[language]`.
-- run the tests suite (create a [development environment](developing.md), then execute `pytest` locally). The tests will generate various text representations corresponding to your notebook under  `tests/notebooks/mirror/`. Please verify that these files are valid scripts, and include them in your PR.
+- contribute a sample notebook in `tests/data/notebooks/inputs/ipynb_[language]`.
+- run the tests suite (create a [development environment](developing.md), then execute `pytest` locally). The tests will generate various text representations corresponding to your notebook under  `tests/data/notebooks/outputs/`. Please verify that these files are valid scripts, and include them in your PR.
diff --git a/docs/using-pre-commit.md b/docs/using-pre-commit.md
@@ -62,5 +62,5 @@ repos:
       language_version: python3
 ```
 
-Tested examples of how to use the pre-commit hook are available in our [tests](https://github.com/mwouts/jupytext/tree/main/tests) -
-see for instance [test_pre_commit_1_sync_with_config.py](https://github.com/mwouts/jupytext/blob/main/tests/test_pre_commit_1_sync_with_config.py).
+Tested examples of how to use the pre-commit hook are available in our [tests](https://github.com/mwouts/jupytext/tree/main/tests/functional/pre-commit) -
+see for instance [test_pre_commit_1_sync_with_config.py](https://github.com/mwouts/jupytext/blob/main/tests/functional/pre-commit/test_pre_commit_1_sync_with_config.py).
diff --git a/pyproject.toml b/pyproject.toml
@@ -46,27 +46,34 @@ Documentation = "https://jupytext.readthedocs.io"
 
 [project.optional-dependencies]
 # Test related dependencies
-# TODO: Split them into unit, integration and functional tests groups
 test = [
-    "autopep8",
-    "black",
-    "isort",
-    "ruff",
-    "flake8",
-    "pytest",
-    "pytest-randomly",
-    "gitpython",
-    "jupyterlab",
-    "notebook",
-    "nbconvert",
-    # jupyter-fs==0.4.0 is async, which is not supported by Jupytext ATM
-    "jupyter-fs<0.4.0",
-    "ipykernel",
-    "pre-commit",
+  "pytest",
+  "pytest-randomly"
+]
+test-integration = [
+  "jupytext[test]",
+  "jupyter-server",
+  "nbconvert"
+]
+test-functional = [
+  "jupytext[test-integration]",
+  # jupytext --pipe and --check
+  "autopep8",
+  "black",
+  "isort",
+  "flake8",
+  # jupytext --execute
+  "ipykernel",
+  # Pre-commit tests
+  "gitpython",
+  "pre-commit",
+  # Interaction with other contents managers
+  # jupyter-fs==0.4.0 is async, which is not supported by Jupytext ATM
+  "jupyter-fs<0.4.0"
 ]
 # Coverage requirements
 test-cov = [
-    "jupytext[test]",
+    "jupytext[test-functional]",
     "pytest-cov>=2.6.1",
 ]
 dev = [
@@ -163,7 +170,7 @@ ignore = ["W002"]
 [tool.ruff]
 line-length = 127
 exclude = [
-    "tests/notebooks/*",
+    "tests/data/notebooks/*",
 ]
 # Seems like W503 is not implemented in ruff
 # ref: https://github.com/astral-sh/ruff/issues/4125
@@ -172,9 +179,32 @@ ignore = [
 ]
 
 [tool.pytest.ini_options]
+markers = [
+    "requires_jupytext",
+    "requires_black",
+    "requires_isort",
+    "requires_flake8",
+    "requires_autopep8",
+    "requires_nbconvert",
+    "requires_myst",
+    "requires_no_myst",
+    "requires_quarto",
+    "requires_pandoc",
+    "requires_no_pandoc",
+    "requires_sphinx_gallery",
+    "requires_user_kernel_python3",
+    "requires_ir_kernel",
+    "skip_on_windows",
+    "pre_commit",
+]
 filterwarnings = [
     # Uncomment this "error" to turn all unfiltered warnings into errors
     # "error",
+    # Jupyter notebook
+    "ignore:Support for bleach <5 will be removed in a future version of nbconvert:DeprecationWarning",
+    # jupyterfs
+    "ignore:run_pre_save_hook is deprecated, use run_pre_save_hooks instead:DeprecationWarning",
+    "ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning",
     # use single quote to denote raw strings in toml
     # (10 warnings)
     'ignore:Passing unrecognized arguments to super\(KernelSpec\).__init__:DeprecationWarning',

diff --git a/src/jupytext/parse_version.py b/src/jupytext/parse_version.py
@@ -1,11 +1,10 @@
 def parse_version(version, custom_error=ImportError):
     try:
-        from pkg_resources import parse_version as parse
+        from packaging.version import parse
     except ImportError:
         try:
-            from packaging.version import parse
+            from pkg_resources import parse_version as parse
         except ImportError:
-            raise custom_error("Please install either pkg_resources or packaging")
+            raise custom_error("Please install either packaging or pkg_resources")
 
-    print(version)
     return parse(version)
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,8 +1,10 @@
+import sys
 import unittest.mock as mock
 from pathlib import Path
 
 import pytest
 from git import Repo
+from jupyter_client.kernelspec import find_kernel_specs, get_kernel_spec
 from nbformat.v4 import nbbase
 from nbformat.v4.nbbase import (
     new_code_cell,
@@ -12,15 +14,28 @@
 )
 
 import jupytext
+from jupytext.cell_reader import rst2md
 from jupytext.cli import system
+from jupytext.myst import is_myst_available
+from jupytext.pandoc import is_pandoc_available
+from jupytext.quarto import is_quarto_available
 
-from .utils import formats_with_support_for_cell_metadata
+from .utils import formats_with_support_for_cell_metadata, tool_version
 
-# Pytest's tmpdir is in /tmp (at least for me), so this helps avoiding interferences between
+# Pytest's tmpdir is in /tmp (at least for me), so this helps to avoid interferences between
 # global configuration on HOME and the test collection
 jupytext.config.JUPYTEXT_CEILING_DIRECTORIES = ["/tmp/"]
 
 
+def isort_version():
+    try:
+        import isort
+
+        return isort.__version__
+    except ImportError:
+        return None
+
+
 @pytest.fixture
 def no_jupytext_version_number():
     with mock.patch("jupytext.header.INSERT_AND_CHECK_VERSION_NUMBER", False):
@@ -107,6 +122,71 @@ def fmt_with_cell_metadata(request):
     return request.param
 
 
+def pytest_runtest_setup(item):
+    for mark in item.iter_markers():
+        for tool in [
+            "jupytext",
+            "black",
+            "isort",
+            "flake8",
+            "autopep8",
+            "jupyter nbconvert",
+        ]:
+            if mark.name == f"requires_{tool.replace(' ', '_')}":
+                if not tool_version(tool):
+                    pytest.skip(f"{tool} is not installed")
+        if mark.name == "requires_sphinx_gallery":
+            if not rst2md:
+                pytest.skip("sphinx_gallery is not available")
+        if mark.name == "requires_pandoc":
+            # The mirror files changed slightly when Pandoc 2.11 was introduced
+            # https://github.com/mwouts/jupytext/commit/c07d919702999056ce47f92b74f63a15c8361c5d
+            # The mirror files changed again when Pandoc 2.16 was introduced
+            # https://github.com/mwouts/jupytext/pull/919/commits/1fa1451ecdaa6ad8d803bcb6fb0c0cf09e5371bf
+            if not is_pandoc_available(min_version="2.16.2", max_version="2.16.2"):
+                pytest.skip("pandoc==2.16.2 is not available")
+        if mark.name == "requires_quarto":
+            if not is_quarto_available(min_version="0.2.0"):
+                pytest.skip("quarto>=0.2 is not available")
+        if mark.name == "requires_no_pandoc":
+            if is_pandoc_available():
+                pytest.skip("Pandoc is installed")
+        if mark.name == "requires_ir_kernel":
+            if not any(
+                get_kernel_spec(name).language == "R" for name in find_kernel_specs()
+            ):
+                pytest.skip("irkernel is not installed")
+        if mark.name == "requires_user_kernel_python3":
+            if "python_kernel" not in find_kernel_specs():
+                pytest.skip(
+                    "Please run 'python -m ipykernel install --name python_kernel --user'"
+                )
+        if mark.name == "requires_myst":
+            if not is_myst_available():
+                pytest.skip("myst_parser not found")
+        if mark.name == "requires_no_myst":
+            if is_myst_available():
+                pytest.skip("myst is available")
+        if mark.name == "skip_on_windows":
+            if sys.platform.startswith("win"):
+                pytest.skip("Issue 489")
+        if mark.name == "pre_commit":
+            if sys.platform.startswith("win"):
+                pytest.skip(
+                    "OSError: [WinError 193] %1 is not a valid Win32 application"
+                )
+            if not (Path(__file__).parent.parent / ".git").is_dir():
+                pytest.skip("Jupytext folder is not a git repository #814")
+
+
+def pytest_collection_modifyitems(config, items):
+    for item in items:
+        if (
+            config.rootdir / "tests" / "functional" / "pre_commit"
+        ) in item.path.parents:
+            item.add_marker(pytest.mark.pre_commit)
+
+
 """To make sure that cell ids are distinct we use a global counter.
     This solves https://github.com/mwouts/jupytext/issues/747"""
 global_cell_count = 0

diff --git a/tests/notebooks/R/simple_r_script.R → ...data/notebooks/inputs/R/simple_r_script.R b/tests/notebooks/R/simple_r_script.R → ...data/notebooks/inputs/R/simple_r_script.R
diff --git a/tests/notebooks/R_spin/knitr-spin.R → ...data/notebooks/inputs/R_spin/knitr-spin.R b/tests/notebooks/R_spin/knitr-spin.R → ...data/notebooks/inputs/R_spin/knitr-spin.R
diff --git a/tests/notebooks/Rmd/R_sample.Rmd → tests/data/notebooks/inputs/Rmd/R_sample.Rmd b/tests/notebooks/Rmd/R_sample.Rmd → tests/data/notebooks/inputs/Rmd/R_sample.Rmd
diff --git a/tests/notebooks/Rmd/chunk_options.Rmd → ...ta/notebooks/inputs/Rmd/chunk_options.Rmd b/tests/notebooks/Rmd/chunk_options.Rmd → ...ta/notebooks/inputs/Rmd/chunk_options.Rmd
diff --git a/tests/notebooks/Rmd/ioslides.Rmd → tests/data/notebooks/inputs/Rmd/ioslides.Rmd b/tests/notebooks/Rmd/ioslides.Rmd → tests/data/notebooks/inputs/Rmd/ioslides.Rmd
diff --git a/tests/notebooks/Rmd/knitr-spin.Rmd → .../data/notebooks/inputs/Rmd/knitr-spin.Rmd b/tests/notebooks/Rmd/knitr-spin.Rmd → .../data/notebooks/inputs/Rmd/knitr-spin.Rmd
diff --git a/tests/notebooks/Rmd/markdown.Rmd → tests/data/notebooks/inputs/Rmd/markdown.Rmd b/tests/notebooks/Rmd/markdown.Rmd → tests/data/notebooks/inputs/Rmd/markdown.Rmd
diff --git a/.../hydrogen/hydrogen_latex_html_R_magics.py → .../hydrogen/hydrogen_latex_html_R_magics.py b/.../hydrogen/hydrogen_latex_html_R_magics.py → .../hydrogen/hydrogen_latex_html_R_magics.py
diff --git a/...R/R notebook with invalid cell keys.ipynb → ...R/R notebook with invalid cell keys.ipynb b/...R/R notebook with invalid cell keys.ipynb → ...R/R notebook with invalid cell keys.ipynb
diff --git a/tests/notebooks/ipynb_R/ir_notebook.ipynb → ...otebooks/inputs/ipynb_R/ir_notebook.ipynb b/tests/notebooks/ipynb_R/ir_notebook.ipynb → ...otebooks/inputs/ipynb_R/ir_notebook.ipynb
diff --git a/...oks/ipynb_bash/sample_bash_notebook.ipynb → ...uts/ipynb_bash/sample_bash_notebook.ipynb b/...oks/ipynb_bash/sample_bash_notebook.ipynb → ...uts/ipynb_bash/sample_bash_notebook.ipynb
diff --git a/...s/notebooks/ipynb_clojure/html-demo.ipynb → ...ooks/inputs/ipynb_clojure/html-demo.ipynb b/...s/notebooks/ipynb_clojure/html-demo.ipynb → ...ooks/inputs/ipynb_clojure/html-demo.ipynb
diff --git a/...ipynb_coconut/coconut_homepage_demo.ipynb → ...ipynb_coconut/coconut_homepage_demo.ipynb b/...ipynb_coconut/coconut_homepage_demo.ipynb → ...ipynb_coconut/coconut_homepage_demo.ipynb
diff --git a/...ebooks/ipynb_cpp/xcpp_by_quantstack.ipynb → ...inputs/ipynb_cpp/xcpp_by_quantstack.ipynb b/...ebooks/ipynb_cpp/xcpp_by_quantstack.ipynb → ...inputs/ipynb_cpp/xcpp_by_quantstack.ipynb
diff --git a/tests/notebooks/ipynb_cs/csharp.ipynb → ...ta/notebooks/inputs/ipynb_cs/csharp.ipynb b/tests/notebooks/ipynb_cs/csharp.ipynb → ...ta/notebooks/inputs/ipynb_cs/csharp.ipynb
diff --git a/tests/notebooks/ipynb_fs/fsharp.ipynb → ...ta/notebooks/inputs/ipynb_fs/fsharp.ipynb b/tests/notebooks/ipynb_fs/fsharp.ipynb → ...ta/notebooks/inputs/ipynb_fs/fsharp.ipynb
diff --git a/...ooks/ipynb_gnuplot/gnuplot_notebook.ipynb → ...puts/ipynb_gnuplot/gnuplot_notebook.ipynb b/...ooks/ipynb_gnuplot/gnuplot_notebook.ipynb → ...puts/ipynb_gnuplot/gnuplot_notebook.ipynb
diff --git a/...pynb_groovy/tailrecursive-factorial.ipynb → ...pynb_groovy/tailrecursive-factorial.ipynb b/...pynb_groovy/tailrecursive-factorial.ipynb → ...pynb_groovy/tailrecursive-factorial.ipynb
diff --git a/...ooks/ipynb_haskell/haskell_notebook.ipynb → ...puts/ipynb_haskell/haskell_notebook.ipynb b/...ooks/ipynb_haskell/haskell_notebook.ipynb → ...puts/ipynb_haskell/haskell_notebook.ipynb
diff --git a/tests/notebooks/ipynb_idl/demo_gdl_fbp.ipynb → ...books/inputs/ipynb_idl/demo_gdl_fbp.ipynb b/tests/notebooks/ipynb_idl/demo_gdl_fbp.ipynb → ...books/inputs/ipynb_idl/demo_gdl_fbp.ipynb
diff --git a/...ebooks/ipynb_java/simple-helloworld.ipynb → ...inputs/ipynb_java/simple-helloworld.ipynb b/...ebooks/ipynb_java/simple-helloworld.ipynb → ...inputs/ipynb_java/simple-helloworld.ipynb
diff --git a/tests/notebooks/ipynb_js/ijavascript.ipynb → ...tebooks/inputs/ipynb_js/ijavascript.ipynb b/tests/notebooks/ipynb_js/ijavascript.ipynb → ...tebooks/inputs/ipynb_js/ijavascript.ipynb
diff --git a/...lia/julia_benchmark_plotly_barchart.ipynb → ...lia/julia_benchmark_plotly_barchart.ipynb b/...lia/julia_benchmark_plotly_barchart.ipynb → ...lia/julia_benchmark_plotly_barchart.ipynb
diff --git a/...ynb_julia/julia_functional_geometry.ipynb → ...ynb_julia/julia_functional_geometry.ipynb b/...ynb_julia/julia_functional_geometry.ipynb → ...ynb_julia/julia_functional_geometry.ipynb
diff --git a/...s/notebooks/ipynb_m/octave_notebook.ipynb → ...ooks/inputs/ipynb_m/octave_notebook.ipynb b/...s/notebooks/ipynb_m/octave_notebook.ipynb → ...ooks/inputs/ipynb_m/octave_notebook.ipynb
diff --git a/...tebooks/ipynb_maxima/maxima_example.ipynb → .../inputs/ipynb_maxima/maxima_example.ipynb b/...tebooks/ipynb_maxima/maxima_example.ipynb → .../inputs/ipynb_maxima/maxima_example.ipynb
diff --git a/...otebooks/ipynb_ocaml/ocaml_notebook.ipynb → ...s/inputs/ipynb_ocaml/ocaml_notebook.ipynb b/...otebooks/ipynb_ocaml/ocaml_notebook.ipynb → ...s/inputs/ipynb_ocaml/ocaml_notebook.ipynb
diff --git a/tests/notebooks/ipynb_ps1/powershell.ipynb → ...tebooks/inputs/ipynb_ps1/powershell.ipynb b/tests/notebooks/ipynb_ps1/powershell.ipynb → ...tebooks/inputs/ipynb_ps1/powershell.ipynb
diff --git a/...s/ipynb_py/Line_breaks_in_LateX_305.ipynb → ...s/ipynb_py/Line_breaks_in_LateX_305.ipynb b/...s/ipynb_py/Line_breaks_in_LateX_305.ipynb → ...s/ipynb_py/Line_breaks_in_LateX_305.ipynb
diff --git a/...with function and cell metadata 164.ipynb → ...with function and cell metadata 164.ipynb b/...with function and cell metadata 164.ipynb → ...with function and cell metadata 164.ipynb
diff --git a/.../Notebook with html and latex cells.ipynb → .../Notebook with html and latex cells.ipynb b/.../Notebook with html and latex cells.ipynb → .../Notebook with html and latex cells.ipynb
diff --git a/...nb_py/Notebook with many hash signs.ipynb → ...nb_py/Notebook with many hash signs.ipynb b/...nb_py/Notebook with many hash signs.ipynb → ...nb_py/Notebook with many hash signs.ipynb
diff --git a/...tebook with metadata and long cells.ipynb → ...tebook with metadata and long cells.ipynb b/...tebook with metadata and long cells.ipynb → ...tebook with metadata and long cells.ipynb
diff --git a/...ooks/ipynb_py/Notebook_with_R_magic.ipynb → ...puts/ipynb_py/Notebook_with_R_magic.ipynb b/...ooks/ipynb_py/Notebook_with_R_magic.ipynb → ...puts/ipynb_py/Notebook_with_R_magic.ipynb
diff --git a/...b_py/Notebook_with_more_R_magic_111.ipynb → ...b_py/Notebook_with_more_R_magic_111.ipynb b/...b_py/Notebook_with_more_R_magic_111.ipynb → ...b_py/Notebook_with_more_R_magic_111.ipynb
diff --git a/...s/ipynb_py/The flavors of raw cells.ipynb → ...s/ipynb_py/The flavors of raw cells.ipynb b/...s/ipynb_py/The flavors of raw cells.ipynb → ...s/ipynb_py/The flavors of raw cells.ipynb
diff --git a/tests/notebooks/ipynb_py/cat_variable.ipynb → ...ebooks/inputs/ipynb_py/cat_variable.ipynb b/tests/notebooks/ipynb_py/cat_variable.ipynb → ...ebooks/inputs/ipynb_py/cat_variable.ipynb
diff --git a/...nvert_to_py_then_test_with_update83.ipynb → ...nvert_to_py_then_test_with_update83.ipynb b/...nvert_to_py_then_test_with_update83.ipynb → ...nvert_to_py_then_test_with_update83.ipynb
diff --git a/tests/notebooks/ipynb_py/frozen_cell.ipynb → ...tebooks/inputs/ipynb_py/frozen_cell.ipynb b/tests/notebooks/ipynb_py/frozen_cell.ipynb → ...tebooks/inputs/ipynb_py/frozen_cell.ipynb
diff --git a/tests/notebooks/ipynb_py/jupyter.ipynb → ...a/notebooks/inputs/ipynb_py/jupyter.ipynb b/tests/notebooks/ipynb_py/jupyter.ipynb → ...a/notebooks/inputs/ipynb_py/jupyter.ipynb
diff --git a/tests/notebooks/ipynb_py/jupyter_again.ipynb → ...books/inputs/ipynb_py/jupyter_again.ipynb b/tests/notebooks/ipynb_py/jupyter_again.ipynb → ...books/inputs/ipynb_py/jupyter_again.ipynb
diff --git a/...nb_py/jupyter_with_raw_cell_in_body.ipynb → ...nb_py/jupyter_with_raw_cell_in_body.ipynb b/...nb_py/jupyter_with_raw_cell_in_body.ipynb → ...nb_py/jupyter_with_raw_cell_in_body.ipynb
diff --git a/...ynb_py/jupyter_with_raw_cell_on_top.ipynb → ...ynb_py/jupyter_with_raw_cell_on_top.ipynb b/...ynb_py/jupyter_with_raw_cell_on_top.ipynb → ...ynb_py/jupyter_with_raw_cell_on_top.ipynb
diff --git a/...b_py/notebook_with_complex_metadata.ipynb → ...b_py/notebook_with_complex_metadata.ipynb b/...b_py/notebook_with_complex_metadata.ipynb → ...b_py/notebook_with_complex_metadata.ipynb
diff --git a/...oks/ipynb_py/nteract_with_parameter.ipynb → ...uts/ipynb_py/nteract_with_parameter.ipynb b/...oks/ipynb_py/nteract_with_parameter.ipynb → ...uts/ipynb_py/nteract_with_parameter.ipynb
diff --git a/tests/notebooks/ipynb_py/plotly_graphs.ipynb → ...books/inputs/ipynb_py/plotly_graphs.ipynb b/tests/notebooks/ipynb_py/plotly_graphs.ipynb → ...books/inputs/ipynb_py/plotly_graphs.ipynb
diff --git a/...ks/ipynb_py/sample_rise_notebook_66.ipynb → ...ts/ipynb_py/sample_rise_notebook_66.ipynb b/...ks/ipynb_py/sample_rise_notebook_66.ipynb → ...ts/ipynb_py/sample_rise_notebook_66.ipynb
diff --git a/...ks/ipynb_py/text_outputs_and_images.ipynb → ...ts/ipynb_py/text_outputs_and_images.ipynb b/...ks/ipynb_py/text_outputs_and_images.ipynb → ...ts/ipynb_py/text_outputs_and_images.ipynb
diff --git a/...b_q/kalman_filter_and_visualization.ipynb → ...b_q/kalman_filter_and_visualization.ipynb b/...b_q/kalman_filter_and_visualization.ipynb → ...b_q/kalman_filter_and_visualization.ipynb
diff --git a/...s/ipynb_robot/simple_robot_notebook.ipynb → ...s/ipynb_robot/simple_robot_notebook.ipynb b/...s/ipynb_robot/simple_robot_notebook.ipynb → ...s/ipynb_robot/simple_robot_notebook.ipynb
diff --git a/...books/ipynb_rust/evcxr_jupyter_tour.ipynb → ...nputs/ipynb_rust/evcxr_jupyter_tour.ipynb b/...books/ipynb_rust/evcxr_jupyter_tour.ipynb → ...nputs/ipynb_rust/evcxr_jupyter_tour.ipynb
diff --git a/...tebooks/ipynb_sage/sage_print_hello.ipynb → .../inputs/ipynb_sage/sage_print_hello.ipynb b/...tebooks/ipynb_sage/sage_print_hello.ipynb → .../inputs/ipynb_sage/sage_print_hello.ipynb
diff --git a/tests/notebooks/ipynb_sas/sas.ipynb → ...data/notebooks/inputs/ipynb_sas/sas.ipynb b/tests/notebooks/ipynb_sas/sas.ipynb → ...data/notebooks/inputs/ipynb_sas/sas.ipynb
diff --git a/...s/ipynb_scala/simple_scala_notebook.ipynb → ...s/ipynb_scala/simple_scala_notebook.ipynb b/...s/ipynb_scala/simple_scala_notebook.ipynb → ...s/ipynb_scala/simple_scala_notebook.ipynb
diff --git a/.../Reference Guide for Calysto Scheme.ipynb → .../Reference Guide for Calysto Scheme.ipynb b/.../Reference Guide for Calysto Scheme.ipynb → .../Reference Guide for Calysto Scheme.ipynb
diff --git a/...ooks/ipynb_sos/jupytext_replication.ipynb → ...puts/ipynb_sos/jupytext_replication.ipynb b/...ooks/ipynb_sos/jupytext_replication.ipynb → ...puts/ipynb_sos/jupytext_replication.ipynb
diff --git a/...otebooks/ipynb_stata/stata_notebook.ipynb → ...s/inputs/ipynb_stata/stata_notebook.ipynb b/...otebooks/ipynb_stata/stata_notebook.ipynb → ...s/inputs/ipynb_stata/stata_notebook.ipynb
diff --git a/tests/notebooks/ipynb_tcl/tcl_test.ipynb → ...notebooks/inputs/ipynb_tcl/tcl_test.ipynb b/tests/notebooks/ipynb_tcl/tcl_test.ipynb → ...notebooks/inputs/ipynb_tcl/tcl_test.ipynb
diff --git a/tests/notebooks/ipynb_ts/itypescript.ipynb → ...tebooks/inputs/ipynb_ts/itypescript.ipynb b/tests/notebooks/ipynb_ts/itypescript.ipynb → ...tebooks/inputs/ipynb_ts/itypescript.ipynb
diff --git a/tests/notebooks/ipynb_wolfram/wolfram.ipynb → ...ebooks/inputs/ipynb_wolfram/wolfram.ipynb b/tests/notebooks/ipynb_wolfram/wolfram.ipynb → ...ebooks/inputs/ipynb_wolfram/wolfram.ipynb
diff --git a/tests/notebooks/julia/julia_sample_script.jl → ...books/inputs/julia/julia_sample_script.jl b/tests/notebooks/julia/julia_sample_script.jl → ...books/inputs/julia/julia_sample_script.jl
diff --git a/tests/notebooks/md/jupytext_markdown.md → .../notebooks/inputs/md/jupytext_markdown.md b/tests/notebooks/md/jupytext_markdown.md → .../notebooks/inputs/md/jupytext_markdown.md
diff --git a/tests/notebooks/md/plain_markdown.md → ...ata/notebooks/inputs/md/plain_markdown.md b/tests/notebooks/md/plain_markdown.md → ...ata/notebooks/inputs/md/plain_markdown.md
diff --git a/tests/notebooks/percent/hydrogen.py → ...data/notebooks/inputs/percent/hydrogen.py b/tests/notebooks/percent/hydrogen.py → ...data/notebooks/inputs/percent/hydrogen.py
diff --git a/tests/notebooks/ps1/build.ps1 → tests/data/notebooks/inputs/ps1/build.ps1 b/tests/notebooks/ps1/build.ps1 → tests/data/notebooks/inputs/ps1/build.ps1
diff --git a/tests/notebooks/python/light_sample.py → ...a/notebooks/inputs/python/light_sample.py b/tests/notebooks/python/light_sample.py → ...a/notebooks/inputs/python/light_sample.py
diff --git a/...otebooks/python/python_notebook_sample.py → ...s/inputs/python/python_notebook_sample.py b/...otebooks/python/python_notebook_sample.py → ...s/inputs/python/python_notebook_sample.py
diff --git a/tests/notebooks/sphinx/plot_notebook.py → .../notebooks/inputs/sphinx/plot_notebook.py b/tests/notebooks/sphinx/plot_notebook.py → .../notebooks/inputs/sphinx/plot_notebook.py
diff --git a/...ebooks/mirror/Rmd_to_ipynb/R_sample.ipynb → ...books/outputs/Rmd_to_ipynb/R_sample.ipynb b/...ebooks/mirror/Rmd_to_ipynb/R_sample.ipynb → ...books/outputs/Rmd_to_ipynb/R_sample.ipynb
diff --git a/...s/mirror/Rmd_to_ipynb/chunk_options.ipynb → .../outputs/Rmd_to_ipynb/chunk_options.ipynb b/...s/mirror/Rmd_to_ipynb/chunk_options.ipynb → .../outputs/Rmd_to_ipynb/chunk_options.ipynb
diff --git a/...ebooks/mirror/Rmd_to_ipynb/ioslides.ipynb → ...books/outputs/Rmd_to_ipynb/ioslides.ipynb b/...ebooks/mirror/Rmd_to_ipynb/ioslides.ipynb → ...books/outputs/Rmd_to_ipynb/ioslides.ipynb
diff --git a/...ooks/mirror/Rmd_to_ipynb/knitr-spin.ipynb → ...oks/outputs/Rmd_to_ipynb/knitr-spin.ipynb b/...ooks/mirror/Rmd_to_ipynb/knitr-spin.ipynb → ...oks/outputs/Rmd_to_ipynb/knitr-spin.ipynb
diff --git a/...ebooks/mirror/Rmd_to_ipynb/markdown.ipynb → ...books/outputs/Rmd_to_ipynb/markdown.ipynb b/...ebooks/mirror/Rmd_to_ipynb/markdown.ipynb → ...books/outputs/Rmd_to_ipynb/markdown.ipynb
diff --git a/...ipynb_to_Rmd/Line_breaks_in_LateX_305.Rmd → ...ipynb_to_Rmd/Line_breaks_in_LateX_305.Rmd b/...ipynb_to_Rmd/Line_breaks_in_LateX_305.Rmd → ...ipynb_to_Rmd/Line_breaks_in_LateX_305.Rmd
diff --git a/...k with function and cell metadata 164.Rmd → ...k with function and cell metadata 164.Rmd b/...k with function and cell metadata 164.Rmd → ...k with function and cell metadata 164.Rmd
diff --git a/...md/Notebook with html and latex cells.Rmd → ...md/Notebook with html and latex cells.Rmd b/...md/Notebook with html and latex cells.Rmd → ...md/Notebook with html and latex cells.Rmd
diff --git a/..._to_Rmd/Notebook with many hash signs.Rmd → ..._to_Rmd/Notebook with many hash signs.Rmd b/..._to_Rmd/Notebook with many hash signs.Rmd → ..._to_Rmd/Notebook with many hash signs.Rmd
diff --git a/...Notebook with metadata and long cells.Rmd → ...Notebook with metadata and long cells.Rmd b/...Notebook with metadata and long cells.Rmd → ...Notebook with metadata and long cells.Rmd
diff --git a/...or/ipynb_to_Rmd/Notebook_with_R_magic.Rmd → ...ts/ipynb_to_Rmd/Notebook_with_R_magic.Rmd b/...or/ipynb_to_Rmd/Notebook_with_R_magic.Rmd → ...ts/ipynb_to_Rmd/Notebook_with_R_magic.Rmd
diff --git a/...to_Rmd/Notebook_with_more_R_magic_111.Rmd → ...to_Rmd/Notebook_with_more_R_magic_111.Rmd b/...to_Rmd/Notebook_with_more_R_magic_111.Rmd → ...to_Rmd/Notebook_with_more_R_magic_111.Rmd
diff --git a/...Rmd/R notebook with invalid cell keys.Rmd → ...Rmd/R notebook with invalid cell keys.Rmd b/...Rmd/R notebook with invalid cell keys.Rmd → ...Rmd/R notebook with invalid cell keys.Rmd
diff --git a/...md/Reference Guide for Calysto Scheme.Rmd → ...md/Reference Guide for Calysto Scheme.Rmd b/...md/Reference Guide for Calysto Scheme.Rmd → ...md/Reference Guide for Calysto Scheme.Rmd
diff --git a/...ipynb_to_Rmd/The flavors of raw cells.Rmd → ...ipynb_to_Rmd/The flavors of raw cells.Rmd b/...ipynb_to_Rmd/The flavors of raw cells.Rmd → ...ipynb_to_Rmd/The flavors of raw cells.Rmd
diff --git a/...ooks/mirror/ipynb_to_Rmd/cat_variable.Rmd → ...oks/outputs/ipynb_to_Rmd/cat_variable.Rmd b/...ooks/mirror/ipynb_to_Rmd/cat_variable.Rmd → ...oks/outputs/ipynb_to_Rmd/cat_variable.Rmd
diff --git a/...or/ipynb_to_Rmd/coconut_homepage_demo.Rmd → ...ts/ipynb_to_Rmd/coconut_homepage_demo.Rmd b/...or/ipynb_to_Rmd/coconut_homepage_demo.Rmd → ...ts/ipynb_to_Rmd/coconut_homepage_demo.Rmd
diff --git a/...convert_to_py_then_test_with_update83.Rmd → ...convert_to_py_then_test_with_update83.Rmd b/...convert_to_py_then_test_with_update83.Rmd → ...convert_to_py_then_test_with_update83.Rmd
diff --git a/.../notebooks/mirror/ipynb_to_Rmd/csharp.Rmd → ...notebooks/outputs/ipynb_to_Rmd/csharp.Rmd b/.../notebooks/mirror/ipynb_to_Rmd/csharp.Rmd → ...notebooks/outputs/ipynb_to_Rmd/csharp.Rmd
diff --git a/...ooks/mirror/ipynb_to_Rmd/demo_gdl_fbp.Rmd → ...oks/outputs/ipynb_to_Rmd/demo_gdl_fbp.Rmd b/...ooks/mirror/ipynb_to_Rmd/demo_gdl_fbp.Rmd → ...oks/outputs/ipynb_to_Rmd/demo_gdl_fbp.Rmd
diff --git a/...irror/ipynb_to_Rmd/evcxr_jupyter_tour.Rmd → ...tputs/ipynb_to_Rmd/evcxr_jupyter_tour.Rmd b/...irror/ipynb_to_Rmd/evcxr_jupyter_tour.Rmd → ...tputs/ipynb_to_Rmd/evcxr_jupyter_tour.Rmd
diff --git a/...books/mirror/ipynb_to_Rmd/frozen_cell.Rmd → ...ooks/outputs/ipynb_to_Rmd/frozen_cell.Rmd b/...books/mirror/ipynb_to_Rmd/frozen_cell.Rmd → ...ooks/outputs/ipynb_to_Rmd/frozen_cell.Rmd
diff --git a/.../notebooks/mirror/ipynb_to_Rmd/fsharp.Rmd → ...notebooks/outputs/ipynb_to_Rmd/fsharp.Rmd b/.../notebooks/mirror/ipynb_to_Rmd/fsharp.Rmd → ...notebooks/outputs/ipynb_to_Rmd/fsharp.Rmd
diff --git a/.../mirror/ipynb_to_Rmd/gnuplot_notebook.Rmd → ...outputs/ipynb_to_Rmd/gnuplot_notebook.Rmd b/.../mirror/ipynb_to_Rmd/gnuplot_notebook.Rmd → ...outputs/ipynb_to_Rmd/gnuplot_notebook.Rmd
diff --git a/.../mirror/ipynb_to_Rmd/haskell_notebook.Rmd → ...outputs/ipynb_to_Rmd/haskell_notebook.Rmd b/.../mirror/ipynb_to_Rmd/haskell_notebook.Rmd → ...outputs/ipynb_to_Rmd/haskell_notebook.Rmd
diff --git a/...tebooks/mirror/ipynb_to_Rmd/html-demo.Rmd → ...ebooks/outputs/ipynb_to_Rmd/html-demo.Rmd b/...tebooks/mirror/ipynb_to_Rmd/html-demo.Rmd → ...ebooks/outputs/ipynb_to_Rmd/html-demo.Rmd
diff --git a/...books/mirror/ipynb_to_Rmd/ijavascript.Rmd → ...ooks/outputs/ipynb_to_Rmd/ijavascript.Rmd b/...books/mirror/ipynb_to_Rmd/ijavascript.Rmd → ...ooks/outputs/ipynb_to_Rmd/ijavascript.Rmd
diff --git a/...books/mirror/ipynb_to_Rmd/ir_notebook.Rmd → ...ooks/outputs/ipynb_to_Rmd/ir_notebook.Rmd b/...books/mirror/ipynb_to_Rmd/ir_notebook.Rmd → ...ooks/outputs/ipynb_to_Rmd/ir_notebook.Rmd
diff --git a/...books/mirror/ipynb_to_Rmd/itypescript.Rmd → ...ooks/outputs/ipynb_to_Rmd/itypescript.Rmd b/...books/mirror/ipynb_to_Rmd/itypescript.Rmd → ...ooks/outputs/ipynb_to_Rmd/itypescript.Rmd
diff --git a/...o_Rmd/julia_benchmark_plotly_barchart.Rmd → ...o_Rmd/julia_benchmark_plotly_barchart.Rmd b/...o_Rmd/julia_benchmark_plotly_barchart.Rmd → ...o_Rmd/julia_benchmark_plotly_barchart.Rmd
diff --git a/...pynb_to_Rmd/julia_functional_geometry.Rmd → ...pynb_to_Rmd/julia_functional_geometry.Rmd b/...pynb_to_Rmd/julia_functional_geometry.Rmd → ...pynb_to_Rmd/julia_functional_geometry.Rmd
diff --git a/...notebooks/mirror/ipynb_to_Rmd/jupyter.Rmd → ...otebooks/outputs/ipynb_to_Rmd/jupyter.Rmd b/...notebooks/mirror/ipynb_to_Rmd/jupyter.Rmd → ...otebooks/outputs/ipynb_to_Rmd/jupyter.Rmd
diff --git a/...oks/mirror/ipynb_to_Rmd/jupyter_again.Rmd → ...ks/outputs/ipynb_to_Rmd/jupyter_again.Rmd b/...oks/mirror/ipynb_to_Rmd/jupyter_again.Rmd → ...ks/outputs/ipynb_to_Rmd/jupyter_again.Rmd
diff --git a/..._to_Rmd/jupyter_with_raw_cell_in_body.Rmd → ..._to_Rmd/jupyter_with_raw_cell_in_body.Rmd b/..._to_Rmd/jupyter_with_raw_cell_in_body.Rmd → ..._to_Rmd/jupyter_with_raw_cell_in_body.Rmd
diff --git a/...b_to_Rmd/jupyter_with_raw_cell_on_top.Rmd → ...b_to_Rmd/jupyter_with_raw_cell_on_top.Rmd b/...b_to_Rmd/jupyter_with_raw_cell_on_top.Rmd → ...b_to_Rmd/jupyter_with_raw_cell_on_top.Rmd
diff --git a/...ror/ipynb_to_Rmd/jupytext_replication.Rmd → ...uts/ipynb_to_Rmd/jupytext_replication.Rmd b/...ror/ipynb_to_Rmd/jupytext_replication.Rmd → ...uts/ipynb_to_Rmd/jupytext_replication.Rmd
diff --git a/...o_Rmd/kalman_filter_and_visualization.Rmd → ...o_Rmd/kalman_filter_and_visualization.Rmd b/...o_Rmd/kalman_filter_and_visualization.Rmd → ...o_Rmd/kalman_filter_and_visualization.Rmd
diff --git a/...ks/mirror/ipynb_to_Rmd/maxima_example.Rmd → ...s/outputs/ipynb_to_Rmd/maxima_example.Rmd b/...ks/mirror/ipynb_to_Rmd/maxima_example.Rmd → ...s/outputs/ipynb_to_Rmd/maxima_example.Rmd
diff --git a/...to_Rmd/notebook_with_complex_metadata.Rmd → ...to_Rmd/notebook_with_complex_metadata.Rmd b/...to_Rmd/notebook_with_complex_metadata.Rmd → ...to_Rmd/notebook_with_complex_metadata.Rmd
diff --git a/...r/ipynb_to_Rmd/nteract_with_parameter.Rmd → ...s/ipynb_to_Rmd/nteract_with_parameter.Rmd b/...r/ipynb_to_Rmd/nteract_with_parameter.Rmd → ...s/ipynb_to_Rmd/nteract_with_parameter.Rmd
diff --git a/...ks/mirror/ipynb_to_Rmd/ocaml_notebook.Rmd → ...s/outputs/ipynb_to_Rmd/ocaml_notebook.Rmd b/...ks/mirror/ipynb_to_Rmd/ocaml_notebook.Rmd → ...s/outputs/ipynb_to_Rmd/ocaml_notebook.Rmd
diff --git a/...s/mirror/ipynb_to_Rmd/octave_notebook.Rmd → .../outputs/ipynb_to_Rmd/octave_notebook.Rmd b/...s/mirror/ipynb_to_Rmd/octave_notebook.Rmd → .../outputs/ipynb_to_Rmd/octave_notebook.Rmd
diff --git a/...oks/mirror/ipynb_to_Rmd/plotly_graphs.Rmd → ...ks/outputs/ipynb_to_Rmd/plotly_graphs.Rmd b/...oks/mirror/ipynb_to_Rmd/plotly_graphs.Rmd → ...ks/outputs/ipynb_to_Rmd/plotly_graphs.Rmd
diff --git a/...ebooks/mirror/ipynb_to_Rmd/powershell.Rmd → ...books/outputs/ipynb_to_Rmd/powershell.Rmd b/...ebooks/mirror/ipynb_to_Rmd/powershell.Rmd → ...books/outputs/ipynb_to_Rmd/powershell.Rmd
diff --git a/.../mirror/ipynb_to_Rmd/sage_print_hello.Rmd → ...outputs/ipynb_to_Rmd/sage_print_hello.Rmd b/.../mirror/ipynb_to_Rmd/sage_print_hello.Rmd → ...outputs/ipynb_to_Rmd/sage_print_hello.Rmd
diff --git a/...ror/ipynb_to_Rmd/sample_bash_notebook.Rmd → ...uts/ipynb_to_Rmd/sample_bash_notebook.Rmd b/...ror/ipynb_to_Rmd/sample_bash_notebook.Rmd → ...uts/ipynb_to_Rmd/sample_bash_notebook.Rmd
diff --git a/.../ipynb_to_Rmd/sample_rise_notebook_66.Rmd → .../ipynb_to_Rmd/sample_rise_notebook_66.Rmd b/.../ipynb_to_Rmd/sample_rise_notebook_66.Rmd → .../ipynb_to_Rmd/sample_rise_notebook_66.Rmd
diff --git a/tests/notebooks/mirror/ipynb_to_Rmd/sas.Rmd → ...ta/notebooks/outputs/ipynb_to_Rmd/sas.Rmd b/tests/notebooks/mirror/ipynb_to_Rmd/sas.Rmd → ...ta/notebooks/outputs/ipynb_to_Rmd/sas.Rmd
diff --git a/...mirror/ipynb_to_Rmd/simple-helloworld.Rmd → ...utputs/ipynb_to_Rmd/simple-helloworld.Rmd b/...mirror/ipynb_to_Rmd/simple-helloworld.Rmd → ...utputs/ipynb_to_Rmd/simple-helloworld.Rmd
diff --git a/...or/ipynb_to_Rmd/simple_robot_notebook.Rmd → ...ts/ipynb_to_Rmd/simple_robot_notebook.Rmd b/...or/ipynb_to_Rmd/simple_robot_notebook.Rmd → ...ts/ipynb_to_Rmd/simple_robot_notebook.Rmd
diff --git a/...or/ipynb_to_Rmd/simple_scala_notebook.Rmd → ...ts/ipynb_to_Rmd/simple_scala_notebook.Rmd b/...or/ipynb_to_Rmd/simple_scala_notebook.Rmd → ...ts/ipynb_to_Rmd/simple_scala_notebook.Rmd
diff --git a/...ks/mirror/ipynb_to_Rmd/stata_notebook.Rmd → ...s/outputs/ipynb_to_Rmd/stata_notebook.Rmd b/...ks/mirror/ipynb_to_Rmd/stata_notebook.Rmd → ...s/outputs/ipynb_to_Rmd/stata_notebook.Rmd
diff --git a/.../ipynb_to_Rmd/tailrecursive-factorial.Rmd → .../ipynb_to_Rmd/tailrecursive-factorial.Rmd b/.../ipynb_to_Rmd/tailrecursive-factorial.Rmd → .../ipynb_to_Rmd/tailrecursive-factorial.Rmd
diff --git a/...otebooks/mirror/ipynb_to_Rmd/tcl_test.Rmd → ...tebooks/outputs/ipynb_to_Rmd/tcl_test.Rmd b/...otebooks/mirror/ipynb_to_Rmd/tcl_test.Rmd → ...tebooks/outputs/ipynb_to_Rmd/tcl_test.Rmd
diff --git a/.../ipynb_to_Rmd/text_outputs_and_images.Rmd → .../ipynb_to_Rmd/text_outputs_and_images.Rmd b/.../ipynb_to_Rmd/text_outputs_and_images.Rmd → .../ipynb_to_Rmd/text_outputs_and_images.Rmd
diff --git a/...notebooks/mirror/ipynb_to_Rmd/wolfram.Rmd → ...otebooks/outputs/ipynb_to_Rmd/wolfram.Rmd b/...notebooks/mirror/ipynb_to_Rmd/wolfram.Rmd → ...otebooks/outputs/ipynb_to_Rmd/wolfram.Rmd
diff --git a/...irror/ipynb_to_Rmd/xcpp_by_quantstack.Rmd → ...tputs/ipynb_to_Rmd/xcpp_by_quantstack.Rmd b/...irror/ipynb_to_Rmd/xcpp_by_quantstack.Rmd → ...tputs/ipynb_to_Rmd/xcpp_by_quantstack.Rmd
diff --git a/...b_to_hydrogen/Line_breaks_in_LateX_305.py → ...b_to_hydrogen/Line_breaks_in_LateX_305.py b/...b_to_hydrogen/Line_breaks_in_LateX_305.py → ...b_to_hydrogen/Line_breaks_in_LateX_305.py
diff --git a/...ok with function and cell metadata 164.py → ...ok with function and cell metadata 164.py b/...ok with function and cell metadata 164.py → ...ok with function and cell metadata 164.py
diff --git a/...gen/Notebook with html and latex cells.py → ...gen/Notebook with html and latex cells.py b/...gen/Notebook with html and latex cells.py → ...gen/Notebook with html and latex cells.py
diff --git a/...hydrogen/Notebook with many hash signs.py → ...hydrogen/Notebook with many hash signs.py b/...hydrogen/Notebook with many hash signs.py → ...hydrogen/Notebook with many hash signs.py
diff --git a/.../Notebook with metadata and long cells.py → .../Notebook with metadata and long cells.py b/.../Notebook with metadata and long cells.py → .../Notebook with metadata and long cells.py
diff --git a/...pynb_to_hydrogen/Notebook_with_R_magic.py → ...pynb_to_hydrogen/Notebook_with_R_magic.py b/...pynb_to_hydrogen/Notebook_with_R_magic.py → ...pynb_to_hydrogen/Notebook_with_R_magic.py
diff --git a/...ydrogen/Notebook_with_more_R_magic_111.py → ...ydrogen/Notebook_with_more_R_magic_111.py b/...ydrogen/Notebook_with_more_R_magic_111.py → ...ydrogen/Notebook_with_more_R_magic_111.py
diff --git a/...rogen/R notebook with invalid cell keys.R → ...rogen/R notebook with invalid cell keys.R b/...rogen/R notebook with invalid cell keys.R → ...rogen/R notebook with invalid cell keys.R
diff --git a/...gen/Reference Guide for Calysto Scheme.ss → ...gen/Reference Guide for Calysto Scheme.ss b/...gen/Reference Guide for Calysto Scheme.ss → ...gen/Reference Guide for Calysto Scheme.ss
diff --git a/...b_to_hydrogen/The flavors of raw cells.py → ...b_to_hydrogen/The flavors of raw cells.py b/...b_to_hydrogen/The flavors of raw cells.py → ...b_to_hydrogen/The flavors of raw cells.py
diff --git a/.../mirror/ipynb_to_hydrogen/cat_variable.py → ...outputs/ipynb_to_hydrogen/cat_variable.py b/.../mirror/ipynb_to_hydrogen/cat_variable.py → ...outputs/ipynb_to_hydrogen/cat_variable.py
diff --git a/...nb_to_hydrogen/coconut_homepage_demo.coco → ...nb_to_hydrogen/coconut_homepage_demo.coco b/...nb_to_hydrogen/coconut_homepage_demo.coco → ...nb_to_hydrogen/coconut_homepage_demo.coco
diff --git a/.../convert_to_py_then_test_with_update83.py → .../convert_to_py_then_test_with_update83.py b/.../convert_to_py_then_test_with_update83.py → .../convert_to_py_then_test_with_update83.py
diff --git a/...ebooks/mirror/ipynb_to_hydrogen/csharp.cs → ...books/outputs/ipynb_to_hydrogen/csharp.cs b/...ebooks/mirror/ipynb_to_hydrogen/csharp.cs → ...books/outputs/ipynb_to_hydrogen/csharp.cs
diff --git a/...mirror/ipynb_to_hydrogen/demo_gdl_fbp.pro → ...utputs/ipynb_to_hydrogen/demo_gdl_fbp.pro b/...mirror/ipynb_to_hydrogen/demo_gdl_fbp.pro → ...utputs/ipynb_to_hydrogen/demo_gdl_fbp.pro
diff --git a/...r/ipynb_to_hydrogen/evcxr_jupyter_tour.rs → ...s/ipynb_to_hydrogen/evcxr_jupyter_tour.rs b/...r/ipynb_to_hydrogen/evcxr_jupyter_tour.rs → ...s/ipynb_to_hydrogen/evcxr_jupyter_tour.rs
diff --git a/...s/mirror/ipynb_to_hydrogen/frozen_cell.py → .../outputs/ipynb_to_hydrogen/frozen_cell.py b/...s/mirror/ipynb_to_hydrogen/frozen_cell.py → .../outputs/ipynb_to_hydrogen/frozen_cell.py
diff --git a/...books/mirror/ipynb_to_hydrogen/fsharp.fsx → ...ooks/outputs/ipynb_to_hydrogen/fsharp.fsx b/...books/mirror/ipynb_to_hydrogen/fsharp.fsx → ...ooks/outputs/ipynb_to_hydrogen/fsharp.fsx
diff --git a/...ror/ipynb_to_hydrogen/gnuplot_notebook.gp → ...uts/ipynb_to_hydrogen/gnuplot_notebook.gp b/...ror/ipynb_to_hydrogen/gnuplot_notebook.gp → ...uts/ipynb_to_hydrogen/gnuplot_notebook.gp
diff --git a/...ror/ipynb_to_hydrogen/haskell_notebook.hs → ...uts/ipynb_to_hydrogen/haskell_notebook.hs b/...ror/ipynb_to_hydrogen/haskell_notebook.hs → ...uts/ipynb_to_hydrogen/haskell_notebook.hs
diff --git a/...ks/mirror/ipynb_to_hydrogen/html-demo.clj → ...s/outputs/ipynb_to_hydrogen/html-demo.clj b/...ks/mirror/ipynb_to_hydrogen/html-demo.clj → ...s/outputs/ipynb_to_hydrogen/html-demo.clj
diff --git a/...s/mirror/ipynb_to_hydrogen/ijavascript.js → .../outputs/ipynb_to_hydrogen/ijavascript.js b/...s/mirror/ipynb_to_hydrogen/ijavascript.js → .../outputs/ipynb_to_hydrogen/ijavascript.js
diff --git a/...ks/mirror/ipynb_to_hydrogen/ir_notebook.R → ...s/outputs/ipynb_to_hydrogen/ir_notebook.R b/...ks/mirror/ipynb_to_hydrogen/ir_notebook.R → ...s/outputs/ipynb_to_hydrogen/ir_notebook.R
diff --git a/...s/mirror/ipynb_to_hydrogen/itypescript.ts → .../outputs/ipynb_to_hydrogen/itypescript.ts b/...s/mirror/ipynb_to_hydrogen/itypescript.ts → .../outputs/ipynb_to_hydrogen/itypescript.ts
diff --git a/...drogen/julia_benchmark_plotly_barchart.jl → ...drogen/julia_benchmark_plotly_barchart.jl b/...drogen/julia_benchmark_plotly_barchart.jl → ...drogen/julia_benchmark_plotly_barchart.jl
diff --git a/..._to_hydrogen/julia_functional_geometry.jl → ..._to_hydrogen/julia_functional_geometry.jl b/..._to_hydrogen/julia_functional_geometry.jl → ..._to_hydrogen/julia_functional_geometry.jl
diff --git a/...books/mirror/ipynb_to_hydrogen/jupyter.py → ...ooks/outputs/ipynb_to_hydrogen/jupyter.py b/...books/mirror/ipynb_to_hydrogen/jupyter.py → ...ooks/outputs/ipynb_to_hydrogen/jupyter.py
diff --git a/...mirror/ipynb_to_hydrogen/jupyter_again.py → ...utputs/ipynb_to_hydrogen/jupyter_again.py b/...mirror/ipynb_to_hydrogen/jupyter_again.py → ...utputs/ipynb_to_hydrogen/jupyter_again.py
diff --git a/...hydrogen/jupyter_with_raw_cell_in_body.py → ...hydrogen/jupyter_with_raw_cell_in_body.py b/...hydrogen/jupyter_with_raw_cell_in_body.py → ...hydrogen/jupyter_with_raw_cell_in_body.py
diff --git a/..._hydrogen/jupyter_with_raw_cell_on_top.py → ..._hydrogen/jupyter_with_raw_cell_on_top.py b/..._hydrogen/jupyter_with_raw_cell_on_top.py → ..._hydrogen/jupyter_with_raw_cell_on_top.py
diff --git a/...pynb_to_hydrogen/jupytext_replication.sos → ...pynb_to_hydrogen/jupytext_replication.sos b/...pynb_to_hydrogen/jupytext_replication.sos → ...pynb_to_hydrogen/jupytext_replication.sos
diff --git a/...ydrogen/kalman_filter_and_visualization.q → ...ydrogen/kalman_filter_and_visualization.q b/...ydrogen/kalman_filter_and_visualization.q → ...ydrogen/kalman_filter_and_visualization.q
diff --git a/...rror/ipynb_to_hydrogen/maxima_example.mac → ...puts/ipynb_to_hydrogen/maxima_example.mac b/...rror/ipynb_to_hydrogen/maxima_example.mac → ...puts/ipynb_to_hydrogen/maxima_example.mac
diff --git a/...ydrogen/notebook_with_complex_metadata.py → ...ydrogen/notebook_with_complex_metadata.py b/...ydrogen/notebook_with_complex_metadata.py → ...ydrogen/notebook_with_complex_metadata.py
diff --git a/...ynb_to_hydrogen/nteract_with_parameter.py → ...ynb_to_hydrogen/nteract_with_parameter.py b/...ynb_to_hydrogen/nteract_with_parameter.py → ...ynb_to_hydrogen/nteract_with_parameter.py
diff --git a/...irror/ipynb_to_hydrogen/ocaml_notebook.ml → ...tputs/ipynb_to_hydrogen/ocaml_notebook.ml b/...irror/ipynb_to_hydrogen/ocaml_notebook.ml → ...tputs/ipynb_to_hydrogen/ocaml_notebook.ml
diff --git a/...irror/ipynb_to_hydrogen/octave_notebook.m → ...tputs/ipynb_to_hydrogen/octave_notebook.m b/...irror/ipynb_to_hydrogen/octave_notebook.m → ...tputs/ipynb_to_hydrogen/octave_notebook.m
diff --git a/...mirror/ipynb_to_hydrogen/plotly_graphs.py → ...utputs/ipynb_to_hydrogen/plotly_graphs.py b/...mirror/ipynb_to_hydrogen/plotly_graphs.py → ...utputs/ipynb_to_hydrogen/plotly_graphs.py
diff --git a/...s/mirror/ipynb_to_hydrogen/powershell.ps1 → .../outputs/ipynb_to_hydrogen/powershell.ps1 b/...s/mirror/ipynb_to_hydrogen/powershell.ps1 → .../outputs/ipynb_to_hydrogen/powershell.ps1
diff --git a/...r/ipynb_to_hydrogen/sage_print_hello.sage → ...s/ipynb_to_hydrogen/sage_print_hello.sage b/...r/ipynb_to_hydrogen/sage_print_hello.sage → ...s/ipynb_to_hydrogen/sage_print_hello.sage
diff --git a/...ipynb_to_hydrogen/sample_bash_notebook.sh → ...ipynb_to_hydrogen/sample_bash_notebook.sh b/...ipynb_to_hydrogen/sample_bash_notebook.sh → ...ipynb_to_hydrogen/sample_bash_notebook.sh
diff --git a/...nb_to_hydrogen/sample_rise_notebook_66.py → ...nb_to_hydrogen/sample_rise_notebook_66.py b/...nb_to_hydrogen/sample_rise_notebook_66.py → ...nb_to_hydrogen/sample_rise_notebook_66.py
diff --git a/...otebooks/mirror/ipynb_to_hydrogen/sas.sas → ...tebooks/outputs/ipynb_to_hydrogen/sas.sas b/...otebooks/mirror/ipynb_to_hydrogen/sas.sas → ...tebooks/outputs/ipynb_to_hydrogen/sas.sas
diff --git a/.../ipynb_to_hydrogen/simple-helloworld.java → .../ipynb_to_hydrogen/simple-helloworld.java b/.../ipynb_to_hydrogen/simple-helloworld.java → .../ipynb_to_hydrogen/simple-helloworld.java
diff --git a/...b_to_hydrogen/simple_robot_notebook.robot → ...b_to_hydrogen/simple_robot_notebook.robot b/...b_to_hydrogen/simple_robot_notebook.robot → ...b_to_hydrogen/simple_robot_notebook.robot
diff --git a/...b_to_hydrogen/simple_scala_notebook.scala → ...b_to_hydrogen/simple_scala_notebook.scala b/...b_to_hydrogen/simple_scala_notebook.scala → ...b_to_hydrogen/simple_scala_notebook.scala
diff --git a/...irror/ipynb_to_hydrogen/stata_notebook.do → ...tputs/ipynb_to_hydrogen/stata_notebook.do b/...irror/ipynb_to_hydrogen/stata_notebook.do → ...tputs/ipynb_to_hydrogen/stata_notebook.do
diff --git a/...o_hydrogen/tailrecursive-factorial.groovy → ...o_hydrogen/tailrecursive-factorial.groovy b/...o_hydrogen/tailrecursive-factorial.groovy → ...o_hydrogen/tailrecursive-factorial.groovy
diff --git a/...oks/mirror/ipynb_to_hydrogen/tcl_test.tcl → ...ks/outputs/ipynb_to_hydrogen/tcl_test.tcl b/...oks/mirror/ipynb_to_hydrogen/tcl_test.tcl → ...ks/outputs/ipynb_to_hydrogen/tcl_test.tcl
diff --git a/...nb_to_hydrogen/text_outputs_and_images.py → ...nb_to_hydrogen/text_outputs_and_images.py b/...nb_to_hydrogen/text_outputs_and_images.py → ...nb_to_hydrogen/text_outputs_and_images.py
diff --git a/.../mirror/ipynb_to_hydrogen/wolfram.wolfram → ...outputs/ipynb_to_hydrogen/wolfram.wolfram b/.../mirror/ipynb_to_hydrogen/wolfram.wolfram → ...outputs/ipynb_to_hydrogen/wolfram.wolfram
diff --git a/.../ipynb_to_hydrogen/xcpp_by_quantstack.cpp → .../ipynb_to_hydrogen/xcpp_by_quantstack.cpp b/.../ipynb_to_hydrogen/xcpp_by_quantstack.cpp → .../ipynb_to_hydrogen/xcpp_by_quantstack.cpp
diff --git a/...r/ipynb_to_md/Line_breaks_in_LateX_305.md → ...s/ipynb_to_md/Line_breaks_in_LateX_305.md b/...r/ipynb_to_md/Line_breaks_in_LateX_305.md → ...s/ipynb_to_md/Line_breaks_in_LateX_305.md
diff --git a/...ok with function and cell metadata 164.md → ...ok with function and cell metadata 164.md b/...ok with function and cell metadata 164.md → ...ok with function and cell metadata 164.md
diff --git a/..._md/Notebook with html and latex cells.md → ..._md/Notebook with html and latex cells.md b/..._md/Notebook with html and latex cells.md → ..._md/Notebook with html and latex cells.md
diff --git a/...nb_to_md/Notebook with many hash signs.md → ...nb_to_md/Notebook with many hash signs.md b/...nb_to_md/Notebook with many hash signs.md → ...nb_to_md/Notebook with many hash signs.md
diff --git a/.../Notebook with metadata and long cells.md → .../Notebook with metadata and long cells.md b/.../Notebook with metadata and long cells.md → .../Notebook with metadata and long cells.md
diff --git a/...rror/ipynb_to_md/Notebook_with_R_magic.md → ...puts/ipynb_to_md/Notebook_with_R_magic.md b/...rror/ipynb_to_md/Notebook_with_R_magic.md → ...puts/ipynb_to_md/Notebook_with_R_magic.md
diff --git a/...b_to_md/Notebook_with_more_R_magic_111.md → ...b_to_md/Notebook_with_more_R_magic_111.md b/...b_to_md/Notebook_with_more_R_magic_111.md → ...b_to_md/Notebook_with_more_R_magic_111.md
diff --git a/...o_md/R notebook with invalid cell keys.md → ...o_md/R notebook with invalid cell keys.md b/...o_md/R notebook with invalid cell keys.md → ...o_md/R notebook with invalid cell keys.md
diff --git a/..._md/Reference Guide for Calysto Scheme.md → ..._md/Reference Guide for Calysto Scheme.md b/..._md/Reference Guide for Calysto Scheme.md → ..._md/Reference Guide for Calysto Scheme.md
diff --git a/...r/ipynb_to_md/The flavors of raw cells.md → ...s/ipynb_to_md/The flavors of raw cells.md b/...r/ipynb_to_md/The flavors of raw cells.md → ...s/ipynb_to_md/The flavors of raw cells.md
diff --git a/...ebooks/mirror/ipynb_to_md/cat_variable.md → ...books/outputs/ipynb_to_md/cat_variable.md b/...ebooks/mirror/ipynb_to_md/cat_variable.md → ...books/outputs/ipynb_to_md/cat_variable.md
diff --git a/...rror/ipynb_to_md/coconut_homepage_demo.md → ...puts/ipynb_to_md/coconut_homepage_demo.md b/...rror/ipynb_to_md/coconut_homepage_demo.md → ...puts/ipynb_to_md/coconut_homepage_demo.md
diff --git a/.../convert_to_py_then_test_with_update83.md → .../convert_to_py_then_test_with_update83.md b/.../convert_to_py_then_test_with_update83.md → .../convert_to_py_then_test_with_update83.md
diff --git a/tests/notebooks/mirror/ipynb_to_md/csharp.md → ...a/notebooks/outputs/ipynb_to_md/csharp.md b/tests/notebooks/mirror/ipynb_to_md/csharp.md → ...a/notebooks/outputs/ipynb_to_md/csharp.md
diff --git a/...ebooks/mirror/ipynb_to_md/demo_gdl_fbp.md → ...books/outputs/ipynb_to_md/demo_gdl_fbp.md b/...ebooks/mirror/ipynb_to_md/demo_gdl_fbp.md → ...books/outputs/ipynb_to_md/demo_gdl_fbp.md
diff --git a/.../mirror/ipynb_to_md/evcxr_jupyter_tour.md → ...outputs/ipynb_to_md/evcxr_jupyter_tour.md b/.../mirror/ipynb_to_md/evcxr_jupyter_tour.md → ...outputs/ipynb_to_md/evcxr_jupyter_tour.md
diff --git a/...tebooks/mirror/ipynb_to_md/frozen_cell.md → ...ebooks/outputs/ipynb_to_md/frozen_cell.md b/...tebooks/mirror/ipynb_to_md/frozen_cell.md → ...ebooks/outputs/ipynb_to_md/frozen_cell.md
diff --git a/tests/notebooks/mirror/ipynb_to_md/fsharp.md → ...a/notebooks/outputs/ipynb_to_md/fsharp.md b/tests/notebooks/mirror/ipynb_to_md/fsharp.md → ...a/notebooks/outputs/ipynb_to_md/fsharp.md
diff --git a/...ks/mirror/ipynb_to_md/gnuplot_notebook.md → ...s/outputs/ipynb_to_md/gnuplot_notebook.md b/...ks/mirror/ipynb_to_md/gnuplot_notebook.md → ...s/outputs/ipynb_to_md/gnuplot_notebook.md
diff --git a/...ks/mirror/ipynb_to_md/haskell_notebook.md → ...s/outputs/ipynb_to_md/haskell_notebook.md b/...ks/mirror/ipynb_to_md/haskell_notebook.md → ...s/outputs/ipynb_to_md/haskell_notebook.md
diff --git a/...notebooks/mirror/ipynb_to_md/html-demo.md → ...otebooks/outputs/ipynb_to_md/html-demo.md b/...notebooks/mirror/ipynb_to_md/html-demo.md → ...otebooks/outputs/ipynb_to_md/html-demo.md
diff --git a/...tebooks/mirror/ipynb_to_md/ijavascript.md → ...ebooks/outputs/ipynb_to_md/ijavascript.md b/...tebooks/mirror/ipynb_to_md/ijavascript.md → ...ebooks/outputs/ipynb_to_md/ijavascript.md
diff --git a/...tebooks/mirror/ipynb_to_md/ir_notebook.md → ...ebooks/outputs/ipynb_to_md/ir_notebook.md b/...tebooks/mirror/ipynb_to_md/ir_notebook.md → ...ebooks/outputs/ipynb_to_md/ir_notebook.md
diff --git a/...tebooks/mirror/ipynb_to_md/itypescript.md → ...ebooks/outputs/ipynb_to_md/itypescript.md b/...tebooks/mirror/ipynb_to_md/itypescript.md → ...ebooks/outputs/ipynb_to_md/itypescript.md
diff --git a/..._to_md/julia_benchmark_plotly_barchart.md → ..._to_md/julia_benchmark_plotly_barchart.md b/..._to_md/julia_benchmark_plotly_barchart.md → ..._to_md/julia_benchmark_plotly_barchart.md
diff --git a/.../ipynb_to_md/julia_functional_geometry.md → .../ipynb_to_md/julia_functional_geometry.md b/.../ipynb_to_md/julia_functional_geometry.md → .../ipynb_to_md/julia_functional_geometry.md
diff --git a/...s/notebooks/mirror/ipynb_to_md/jupyter.md → .../notebooks/outputs/ipynb_to_md/jupyter.md b/...s/notebooks/mirror/ipynb_to_md/jupyter.md → .../notebooks/outputs/ipynb_to_md/jupyter.md
diff --git a/...books/mirror/ipynb_to_md/jupyter_again.md → ...ooks/outputs/ipynb_to_md/jupyter_again.md b/...books/mirror/ipynb_to_md/jupyter_again.md → ...ooks/outputs/ipynb_to_md/jupyter_again.md
diff --git a/...nb_to_md/jupyter_with_raw_cell_in_body.md → ...nb_to_md/jupyter_with_raw_cell_in_body.md b/...nb_to_md/jupyter_with_raw_cell_in_body.md → ...nb_to_md/jupyter_with_raw_cell_in_body.md
diff --git a/...ynb_to_md/jupyter_with_raw_cell_on_top.md → ...ynb_to_md/jupyter_with_raw_cell_on_top.md b/...ynb_to_md/jupyter_with_raw_cell_on_top.md → ...ynb_to_md/jupyter_with_raw_cell_on_top.md
diff --git a/...irror/ipynb_to_md/jupytext_replication.md → ...tputs/ipynb_to_md/jupytext_replication.md b/...irror/ipynb_to_md/jupytext_replication.md → ...tputs/ipynb_to_md/jupytext_replication.md
diff --git a/..._to_md/kalman_filter_and_visualization.md → ..._to_md/kalman_filter_and_visualization.md b/..._to_md/kalman_filter_and_visualization.md → ..._to_md/kalman_filter_and_visualization.md
diff --git a/...ooks/mirror/ipynb_to_md/maxima_example.md → ...oks/outputs/ipynb_to_md/maxima_example.md b/...ooks/mirror/ipynb_to_md/maxima_example.md → ...oks/outputs/ipynb_to_md/maxima_example.md
diff --git a/...b_to_md/notebook_with_complex_metadata.md → ...b_to_md/notebook_with_complex_metadata.md b/...b_to_md/notebook_with_complex_metadata.md → ...b_to_md/notebook_with_complex_metadata.md
diff --git a/...ror/ipynb_to_md/nteract_with_parameter.md → ...uts/ipynb_to_md/nteract_with_parameter.md b/...ror/ipynb_to_md/nteract_with_parameter.md → ...uts/ipynb_to_md/nteract_with_parameter.md
diff --git a/...ooks/mirror/ipynb_to_md/ocaml_notebook.md → ...oks/outputs/ipynb_to_md/ocaml_notebook.md b/...ooks/mirror/ipynb_to_md/ocaml_notebook.md → ...oks/outputs/ipynb_to_md/ocaml_notebook.md
diff --git a/...oks/mirror/ipynb_to_md/octave_notebook.md → ...ks/outputs/ipynb_to_md/octave_notebook.md b/...oks/mirror/ipynb_to_md/octave_notebook.md → ...ks/outputs/ipynb_to_md/octave_notebook.md
diff --git a/...books/mirror/ipynb_to_md/plotly_graphs.md → ...ooks/outputs/ipynb_to_md/plotly_graphs.md b/...books/mirror/ipynb_to_md/plotly_graphs.md → ...ooks/outputs/ipynb_to_md/plotly_graphs.md
diff --git a/...otebooks/mirror/ipynb_to_md/powershell.md → ...tebooks/outputs/ipynb_to_md/powershell.md b/...otebooks/mirror/ipynb_to_md/powershell.md → ...tebooks/outputs/ipynb_to_md/powershell.md
diff --git a/...ks/mirror/ipynb_to_md/sage_print_hello.md → ...s/outputs/ipynb_to_md/sage_print_hello.md b/...ks/mirror/ipynb_to_md/sage_print_hello.md → ...s/outputs/ipynb_to_md/sage_print_hello.md
diff --git a/...irror/ipynb_to_md/sample_bash_notebook.md → ...tputs/ipynb_to_md/sample_bash_notebook.md b/...irror/ipynb_to_md/sample_bash_notebook.md → ...tputs/ipynb_to_md/sample_bash_notebook.md
diff --git a/...or/ipynb_to_md/sample_rise_notebook_66.md → ...ts/ipynb_to_md/sample_rise_notebook_66.md b/...or/ipynb_to_md/sample_rise_notebook_66.md → ...ts/ipynb_to_md/sample_rise_notebook_66.md
diff --git a/tests/notebooks/mirror/ipynb_to_md/sas.md → ...data/notebooks/outputs/ipynb_to_md/sas.md b/tests/notebooks/mirror/ipynb_to_md/sas.md → ...data/notebooks/outputs/ipynb_to_md/sas.md
diff --git a/...s/mirror/ipynb_to_md/simple-helloworld.md → .../outputs/ipynb_to_md/simple-helloworld.md b/...s/mirror/ipynb_to_md/simple-helloworld.md → .../outputs/ipynb_to_md/simple-helloworld.md
diff --git a/...rror/ipynb_to_md/simple_robot_notebook.md → ...puts/ipynb_to_md/simple_robot_notebook.md b/...rror/ipynb_to_md/simple_robot_notebook.md → ...puts/ipynb_to_md/simple_robot_notebook.md
diff --git a/...rror/ipynb_to_md/simple_scala_notebook.md → ...puts/ipynb_to_md/simple_scala_notebook.md b/...rror/ipynb_to_md/simple_scala_notebook.md → ...puts/ipynb_to_md/simple_scala_notebook.md
diff --git a/...ooks/mirror/ipynb_to_md/stata_notebook.md → ...oks/outputs/ipynb_to_md/stata_notebook.md b/...ooks/mirror/ipynb_to_md/stata_notebook.md → ...oks/outputs/ipynb_to_md/stata_notebook.md
diff --git a/...or/ipynb_to_md/tailrecursive-factorial.md → ...ts/ipynb_to_md/tailrecursive-factorial.md b/...or/ipynb_to_md/tailrecursive-factorial.md → ...ts/ipynb_to_md/tailrecursive-factorial.md
diff --git a/.../notebooks/mirror/ipynb_to_md/tcl_test.md → ...notebooks/outputs/ipynb_to_md/tcl_test.md b/.../notebooks/mirror/ipynb_to_md/tcl_test.md → ...notebooks/outputs/ipynb_to_md/tcl_test.md
diff --git a/...or/ipynb_to_md/text_outputs_and_images.md → ...ts/ipynb_to_md/text_outputs_and_images.md b/...or/ipynb_to_md/text_outputs_and_images.md → ...ts/ipynb_to_md/text_outputs_and_images.md
diff --git a/...s/notebooks/mirror/ipynb_to_md/wolfram.md → .../notebooks/outputs/ipynb_to_md/wolfram.md b/...s/notebooks/mirror/ipynb_to_md/wolfram.md → .../notebooks/outputs/ipynb_to_md/wolfram.md
diff --git a/.../mirror/ipynb_to_md/xcpp_by_quantstack.md → ...outputs/ipynb_to_md/xcpp_by_quantstack.md b/.../mirror/ipynb_to_md/xcpp_by_quantstack.md → ...outputs/ipynb_to_md/xcpp_by_quantstack.md
diff --git a/...ipynb_to_myst/Line_breaks_in_LateX_305.md → ...ipynb_to_myst/Line_breaks_in_LateX_305.md b/...ipynb_to_myst/Line_breaks_in_LateX_305.md → ...ipynb_to_myst/Line_breaks_in_LateX_305.md
diff --git a/...ok with function and cell metadata 164.md → ...ok with function and cell metadata 164.md b/...ok with function and cell metadata 164.md → ...ok with function and cell metadata 164.md
diff --git a/...yst/Notebook with html and latex cells.md → ...yst/Notebook with html and latex cells.md b/...yst/Notebook with html and latex cells.md → ...yst/Notebook with html and latex cells.md
diff --git a/..._to_myst/Notebook with many hash signs.md → ..._to_myst/Notebook with many hash signs.md b/..._to_myst/Notebook with many hash signs.md → ..._to_myst/Notebook with many hash signs.md
diff --git a/.../Notebook with metadata and long cells.md → .../Notebook with metadata and long cells.md b/.../Notebook with metadata and long cells.md → .../Notebook with metadata and long cells.md
diff --git a/...or/ipynb_to_myst/Notebook_with_R_magic.md → ...ts/ipynb_to_myst/Notebook_with_R_magic.md b/...or/ipynb_to_myst/Notebook_with_R_magic.md → ...ts/ipynb_to_myst/Notebook_with_R_magic.md
diff --git a/...to_myst/Notebook_with_more_R_magic_111.md → ...to_myst/Notebook_with_more_R_magic_111.md b/...to_myst/Notebook_with_more_R_magic_111.md → ...to_myst/Notebook_with_more_R_magic_111.md
diff --git a/...myst/R notebook with invalid cell keys.md → ...myst/R notebook with invalid cell keys.md b/...myst/R notebook with invalid cell keys.md → ...myst/R notebook with invalid cell keys.md
diff --git a/...yst/Reference Guide for Calysto Scheme.md → ...yst/Reference Guide for Calysto Scheme.md b/...yst/Reference Guide for Calysto Scheme.md → ...yst/Reference Guide for Calysto Scheme.md
diff --git a/...ipynb_to_myst/The flavors of raw cells.md → ...ipynb_to_myst/The flavors of raw cells.md b/...ipynb_to_myst/The flavors of raw cells.md → ...ipynb_to_myst/The flavors of raw cells.md
diff --git a/...ooks/mirror/ipynb_to_myst/cat_variable.md → ...oks/outputs/ipynb_to_myst/cat_variable.md b/...ooks/mirror/ipynb_to_myst/cat_variable.md → ...oks/outputs/ipynb_to_myst/cat_variable.md
diff --git a/...or/ipynb_to_myst/coconut_homepage_demo.md → ...ts/ipynb_to_myst/coconut_homepage_demo.md b/...or/ipynb_to_myst/coconut_homepage_demo.md → ...ts/ipynb_to_myst/coconut_homepage_demo.md
diff --git a/.../convert_to_py_then_test_with_update83.md → .../convert_to_py_then_test_with_update83.md b/.../convert_to_py_then_test_with_update83.md → .../convert_to_py_then_test_with_update83.md
diff --git a/.../notebooks/mirror/ipynb_to_myst/csharp.md → ...notebooks/outputs/ipynb_to_myst/csharp.md b/.../notebooks/mirror/ipynb_to_myst/csharp.md → ...notebooks/outputs/ipynb_to_myst/csharp.md
diff --git a/...ooks/mirror/ipynb_to_myst/demo_gdl_fbp.md → ...oks/outputs/ipynb_to_myst/demo_gdl_fbp.md b/...ooks/mirror/ipynb_to_myst/demo_gdl_fbp.md → ...oks/outputs/ipynb_to_myst/demo_gdl_fbp.md
diff --git a/...irror/ipynb_to_myst/evcxr_jupyter_tour.md → ...tputs/ipynb_to_myst/evcxr_jupyter_tour.md b/...irror/ipynb_to_myst/evcxr_jupyter_tour.md → ...tputs/ipynb_to_myst/evcxr_jupyter_tour.md
diff --git a/...books/mirror/ipynb_to_myst/frozen_cell.md → ...ooks/outputs/ipynb_to_myst/frozen_cell.md b/...books/mirror/ipynb_to_myst/frozen_cell.md → ...ooks/outputs/ipynb_to_myst/frozen_cell.md
diff --git a/.../notebooks/mirror/ipynb_to_myst/fsharp.md → ...notebooks/outputs/ipynb_to_myst/fsharp.md b/.../notebooks/mirror/ipynb_to_myst/fsharp.md → ...notebooks/outputs/ipynb_to_myst/fsharp.md
diff --git a/.../mirror/ipynb_to_myst/gnuplot_notebook.md → ...outputs/ipynb_to_myst/gnuplot_notebook.md b/.../mirror/ipynb_to_myst/gnuplot_notebook.md → ...outputs/ipynb_to_myst/gnuplot_notebook.md
diff --git a/.../mirror/ipynb_to_myst/haskell_notebook.md → ...outputs/ipynb_to_myst/haskell_notebook.md b/.../mirror/ipynb_to_myst/haskell_notebook.md → ...outputs/ipynb_to_myst/haskell_notebook.md
diff --git a/...books/mirror/ipynb_to_myst/ijavascript.md → ...ooks/outputs/ipynb_to_myst/ijavascript.md b/...books/mirror/ipynb_to_myst/ijavascript.md → ...ooks/outputs/ipynb_to_myst/ijavascript.md
diff --git a/...books/mirror/ipynb_to_myst/ir_notebook.md → ...ooks/outputs/ipynb_to_myst/ir_notebook.md b/...books/mirror/ipynb_to_myst/ir_notebook.md → ...ooks/outputs/ipynb_to_myst/ir_notebook.md
diff --git a/...books/mirror/ipynb_to_myst/itypescript.md → ...ooks/outputs/ipynb_to_myst/itypescript.md b/...books/mirror/ipynb_to_myst/itypescript.md → ...ooks/outputs/ipynb_to_myst/itypescript.md
diff --git a/...o_myst/julia_benchmark_plotly_barchart.md → ...o_myst/julia_benchmark_plotly_barchart.md b/...o_myst/julia_benchmark_plotly_barchart.md → ...o_myst/julia_benchmark_plotly_barchart.md
diff --git a/...notebooks/mirror/ipynb_to_myst/jupyter.md → ...otebooks/outputs/ipynb_to_myst/jupyter.md b/...notebooks/mirror/ipynb_to_myst/jupyter.md → ...otebooks/outputs/ipynb_to_myst/jupyter.md
diff --git a/...oks/mirror/ipynb_to_myst/jupyter_again.md → ...ks/outputs/ipynb_to_myst/jupyter_again.md b/...oks/mirror/ipynb_to_myst/jupyter_again.md → ...ks/outputs/ipynb_to_myst/jupyter_again.md
diff --git a/..._to_myst/jupyter_with_raw_cell_in_body.md → ..._to_myst/jupyter_with_raw_cell_in_body.md b/..._to_myst/jupyter_with_raw_cell_in_body.md → ..._to_myst/jupyter_with_raw_cell_in_body.md
diff --git a/...b_to_myst/jupyter_with_raw_cell_on_top.md → ...b_to_myst/jupyter_with_raw_cell_on_top.md b/...b_to_myst/jupyter_with_raw_cell_on_top.md → ...b_to_myst/jupyter_with_raw_cell_on_top.md
diff --git a/...ror/ipynb_to_myst/jupytext_replication.md → ...uts/ipynb_to_myst/jupytext_replication.md b/...ror/ipynb_to_myst/jupytext_replication.md → ...uts/ipynb_to_myst/jupytext_replication.md
diff --git a/...o_myst/kalman_filter_and_visualization.md → ...o_myst/kalman_filter_and_visualization.md b/...o_myst/kalman_filter_and_visualization.md → ...o_myst/kalman_filter_and_visualization.md
diff --git a/...ks/mirror/ipynb_to_myst/maxima_example.md → ...s/outputs/ipynb_to_myst/maxima_example.md b/...ks/mirror/ipynb_to_myst/maxima_example.md → ...s/outputs/ipynb_to_myst/maxima_example.md
diff --git a/...to_myst/notebook_with_complex_metadata.md → ...to_myst/notebook_with_complex_metadata.md b/...to_myst/notebook_with_complex_metadata.md → ...to_myst/notebook_with_complex_metadata.md
diff --git a/...r/ipynb_to_myst/nteract_with_parameter.md → ...s/ipynb_to_myst/nteract_with_parameter.md b/...r/ipynb_to_myst/nteract_with_parameter.md → ...s/ipynb_to_myst/nteract_with_parameter.md
diff --git a/...ks/mirror/ipynb_to_myst/ocaml_notebook.md → ...s/outputs/ipynb_to_myst/ocaml_notebook.md b/...ks/mirror/ipynb_to_myst/ocaml_notebook.md → ...s/outputs/ipynb_to_myst/ocaml_notebook.md
diff --git a/...s/mirror/ipynb_to_myst/octave_notebook.md → .../outputs/ipynb_to_myst/octave_notebook.md b/...s/mirror/ipynb_to_myst/octave_notebook.md → .../outputs/ipynb_to_myst/octave_notebook.md
diff --git a/...oks/mirror/ipynb_to_myst/plotly_graphs.md → ...ks/outputs/ipynb_to_myst/plotly_graphs.md b/...oks/mirror/ipynb_to_myst/plotly_graphs.md → ...ks/outputs/ipynb_to_myst/plotly_graphs.md
diff --git a/...ebooks/mirror/ipynb_to_myst/powershell.md → ...books/outputs/ipynb_to_myst/powershell.md b/...ebooks/mirror/ipynb_to_myst/powershell.md → ...books/outputs/ipynb_to_myst/powershell.md
diff --git a/.../mirror/ipynb_to_myst/sage_print_hello.md → ...outputs/ipynb_to_myst/sage_print_hello.md b/.../mirror/ipynb_to_myst/sage_print_hello.md → ...outputs/ipynb_to_myst/sage_print_hello.md
diff --git a/...ror/ipynb_to_myst/sample_bash_notebook.md → ...uts/ipynb_to_myst/sample_bash_notebook.md b/...ror/ipynb_to_myst/sample_bash_notebook.md → ...uts/ipynb_to_myst/sample_bash_notebook.md
diff --git a/.../ipynb_to_myst/sample_rise_notebook_66.md → .../ipynb_to_myst/sample_rise_notebook_66.md b/.../ipynb_to_myst/sample_rise_notebook_66.md → .../ipynb_to_myst/sample_rise_notebook_66.md
diff --git a/tests/notebooks/mirror/ipynb_to_myst/sas.md → ...ta/notebooks/outputs/ipynb_to_myst/sas.md b/tests/notebooks/mirror/ipynb_to_myst/sas.md → ...ta/notebooks/outputs/ipynb_to_myst/sas.md
diff --git a/...mirror/ipynb_to_myst/simple-helloworld.md → ...utputs/ipynb_to_myst/simple-helloworld.md b/...mirror/ipynb_to_myst/simple-helloworld.md → ...utputs/ipynb_to_myst/simple-helloworld.md
diff --git a/...or/ipynb_to_myst/simple_robot_notebook.md → ...ts/ipynb_to_myst/simple_robot_notebook.md b/...or/ipynb_to_myst/simple_robot_notebook.md → ...ts/ipynb_to_myst/simple_robot_notebook.md
diff --git a/...or/ipynb_to_myst/simple_scala_notebook.md → ...ts/ipynb_to_myst/simple_scala_notebook.md b/...or/ipynb_to_myst/simple_scala_notebook.md → ...ts/ipynb_to_myst/simple_scala_notebook.md
diff --git a/...ks/mirror/ipynb_to_myst/stata_notebook.md → ...s/outputs/ipynb_to_myst/stata_notebook.md b/...ks/mirror/ipynb_to_myst/stata_notebook.md → ...s/outputs/ipynb_to_myst/stata_notebook.md
diff --git a/.../ipynb_to_myst/tailrecursive-factorial.md → .../ipynb_to_myst/tailrecursive-factorial.md b/.../ipynb_to_myst/tailrecursive-factorial.md → .../ipynb_to_myst/tailrecursive-factorial.md
diff --git a/...otebooks/mirror/ipynb_to_myst/tcl_test.md → ...tebooks/outputs/ipynb_to_myst/tcl_test.md b/...otebooks/mirror/ipynb_to_myst/tcl_test.md → ...tebooks/outputs/ipynb_to_myst/tcl_test.md
diff --git a/.../ipynb_to_myst/text_outputs_and_images.md → .../ipynb_to_myst/text_outputs_and_images.md b/.../ipynb_to_myst/text_outputs_and_images.md → .../ipynb_to_myst/text_outputs_and_images.md
diff --git a/...notebooks/mirror/ipynb_to_myst/wolfram.md → ...otebooks/outputs/ipynb_to_myst/wolfram.md b/...notebooks/mirror/ipynb_to_myst/wolfram.md → ...otebooks/outputs/ipynb_to_myst/wolfram.md
diff --git a/.../ipynb_to_pandoc/Notebook_with_R_magic.md → .../ipynb_to_pandoc/Notebook_with_R_magic.md b/.../ipynb_to_pandoc/Notebook_with_R_magic.md → .../ipynb_to_pandoc/Notebook_with_R_magic.md
diff --git a/..._pandoc/Notebook_with_more_R_magic_111.md → ..._pandoc/Notebook_with_more_R_magic_111.md b/..._pandoc/Notebook_with_more_R_magic_111.md → ..._pandoc/Notebook_with_more_R_magic_111.md
diff --git a/...ks/mirror/ipynb_to_pandoc/cat_variable.md → ...s/outputs/ipynb_to_pandoc/cat_variable.md b/...ks/mirror/ipynb_to_pandoc/cat_variable.md → ...s/outputs/ipynb_to_pandoc/cat_variable.md
diff --git a/.../convert_to_py_then_test_with_update83.md → .../convert_to_py_then_test_with_update83.md b/.../convert_to_py_then_test_with_update83.md → .../convert_to_py_then_test_with_update83.md
diff --git a/...oks/mirror/ipynb_to_pandoc/frozen_cell.md → ...ks/outputs/ipynb_to_pandoc/frozen_cell.md b/...oks/mirror/ipynb_to_pandoc/frozen_cell.md → ...ks/outputs/ipynb_to_pandoc/frozen_cell.md
diff --git a/...oks/mirror/ipynb_to_pandoc/ir_notebook.md → ...ks/outputs/ipynb_to_pandoc/ir_notebook.md b/...oks/mirror/ipynb_to_pandoc/ir_notebook.md → ...ks/outputs/ipynb_to_pandoc/ir_notebook.md
diff --git a/...pandoc/julia_benchmark_plotly_barchart.md → ...pandoc/julia_benchmark_plotly_barchart.md b/...pandoc/julia_benchmark_plotly_barchart.md → ...pandoc/julia_benchmark_plotly_barchart.md
diff --git a/...tebooks/mirror/ipynb_to_pandoc/jupyter.md → ...ebooks/outputs/ipynb_to_pandoc/jupyter.md b/...tebooks/mirror/ipynb_to_pandoc/jupyter.md → ...ebooks/outputs/ipynb_to_pandoc/jupyter.md
diff --git a/...s/mirror/ipynb_to_pandoc/jupyter_again.md → .../outputs/ipynb_to_pandoc/jupyter_again.md b/...s/mirror/ipynb_to_pandoc/jupyter_again.md → .../outputs/ipynb_to_pandoc/jupyter_again.md
diff --git a/...o_pandoc/jupyter_with_raw_cell_in_body.md → ...o_pandoc/jupyter_with_raw_cell_in_body.md b/...o_pandoc/jupyter_with_raw_cell_in_body.md → ...o_pandoc/jupyter_with_raw_cell_in_body.md
diff --git a/...to_pandoc/jupyter_with_raw_cell_on_top.md → ...to_pandoc/jupyter_with_raw_cell_on_top.md b/...to_pandoc/jupyter_with_raw_cell_on_top.md → ...to_pandoc/jupyter_with_raw_cell_on_top.md
diff --git a/..._pandoc/notebook_with_complex_metadata.md → ..._pandoc/notebook_with_complex_metadata.md b/..._pandoc/notebook_with_complex_metadata.md → ..._pandoc/notebook_with_complex_metadata.md
diff --git a/...ipynb_to_pandoc/nteract_with_parameter.md → ...ipynb_to_pandoc/nteract_with_parameter.md b/...ipynb_to_pandoc/nteract_with_parameter.md → ...ipynb_to_pandoc/nteract_with_parameter.md
diff --git a/...s/mirror/ipynb_to_pandoc/plotly_graphs.md → .../outputs/ipynb_to_pandoc/plotly_graphs.md b/...s/mirror/ipynb_to_pandoc/plotly_graphs.md → .../outputs/ipynb_to_pandoc/plotly_graphs.md
diff --git a/...pynb_to_pandoc/sample_rise_notebook_66.md → ...pynb_to_pandoc/sample_rise_notebook_66.md b/...pynb_to_pandoc/sample_rise_notebook_66.md → ...pynb_to_pandoc/sample_rise_notebook_66.md