Revise dandi-cli to conform for linc-cli

lincbrain · Nov 27, 2023 · 062cbc5 · 062cbc5
1 parent 80114bc
commit 062cbc5
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Showing 104 changed files with 11 additions and 14 deletions.
diff --git a/.pypirc b/.pypirc
@@ -1,3 +0,0 @@
-[pypi]
-username = __token__
-password = pypi-AgEIcHlwaS5vcmcCJDE3MjMzZDczLTExM2QtNGY0ZS1iMmY0LTcxNGM3NTY5NGU0NQACKlszLCI3MDM5NDU5Yi05ZjkzLTQ0ZjYtYWZlMS02MTU3MTNmNzU2ZDkiXQAABiC4dolGR5CXL5UHbRoyh4UEi9b8T0U3l7jL1eS6EeaCgw

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -17,15 +17,15 @@
 
 # -- Project information -----------------------------------------------------
 
-import dandi
+import lincbrain
 
-project = "dandi"
+project = "lincbrain"
 copyright = "2021-2023, DANDI Team"
 author = "DANDI Team"
 
 # The full version, including alpha/beta/rc tags
-version = dandi.__version__
-release = dandi.__version__
+version = lincbrain.__version__
+release = lincbrain.__version__
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/examples/dandiapi-as_readable.py b/docs/source/examples/dandiapi-as_readable.py
@@ -1,4 +1,4 @@
-from dandi.dandiapi import DandiAPIClient
+from lincbrain.dandiapi import DandiAPIClient
 
 dandiset_id = "000006"  # ephys dataset from the Svoboda Lab
 filepath = "sub-anm372795/sub-anm372795_ses-20170718.nwb"  # 450 kB file

diff --git a/docs/source/examples/dandiapi-example.py b/docs/source/examples/dandiapi-example.py
@@ -1,6 +1,6 @@
 import json
 
-from dandi.dandiapi import DandiAPIClient
+from lincbrain.dandiapi import DandiAPIClient
 
 with DandiAPIClient.for_dandi_instance("dandi") as client:
     for dandiset in client.get_dandisets():

diff --git a/dandi/__init__.py → lincbrain/__init__.py b/dandi/__init__.py → lincbrain/__init__.py
diff --git a/dandi/_version.py → lincbrain/_version.py b/dandi/_version.py → lincbrain/_version.py
diff --git a/dandi/cli/__init__.py → lincbrain/cli/__init__.py b/dandi/cli/__init__.py → lincbrain/cli/__init__.py
diff --git a/dandi/cli/base.py → lincbrain/cli/base.py b/dandi/cli/base.py → lincbrain/cli/base.py
diff --git a/dandi/cli/cmd_delete.py → lincbrain/cli/cmd_delete.py b/dandi/cli/cmd_delete.py → lincbrain/cli/cmd_delete.py
diff --git a/dandi/cli/cmd_digest.py → lincbrain/cli/cmd_digest.py b/dandi/cli/cmd_digest.py → lincbrain/cli/cmd_digest.py
diff --git a/dandi/cli/cmd_download.py → lincbrain/cli/cmd_download.py b/dandi/cli/cmd_download.py → lincbrain/cli/cmd_download.py
diff --git a/dandi/cli/cmd_instances.py → lincbrain/cli/cmd_instances.py b/dandi/cli/cmd_instances.py → lincbrain/cli/cmd_instances.py
diff --git a/dandi/cli/cmd_ls.py → lincbrain/cli/cmd_ls.py b/dandi/cli/cmd_ls.py → lincbrain/cli/cmd_ls.py
diff --git a/dandi/cli/cmd_move.py → lincbrain/cli/cmd_move.py b/dandi/cli/cmd_move.py → lincbrain/cli/cmd_move.py
diff --git a/dandi/cli/cmd_organize.py → lincbrain/cli/cmd_organize.py b/dandi/cli/cmd_organize.py → lincbrain/cli/cmd_organize.py
diff --git a/dandi/cli/cmd_service_scripts.py → lincbrain/cli/cmd_service_scripts.py b/dandi/cli/cmd_service_scripts.py → lincbrain/cli/cmd_service_scripts.py
diff --git a/dandi/cli/cmd_shell_completion.py → lincbrain/cli/cmd_shell_completion.py b/dandi/cli/cmd_shell_completion.py → lincbrain/cli/cmd_shell_completion.py
diff --git a/dandi/cli/cmd_upload.py → lincbrain/cli/cmd_upload.py b/dandi/cli/cmd_upload.py → lincbrain/cli/cmd_upload.py
diff --git a/dandi/cli/cmd_validate.py → lincbrain/cli/cmd_validate.py b/dandi/cli/cmd_validate.py → lincbrain/cli/cmd_validate.py
diff --git a/dandi/cli/command.py → lincbrain/cli/command.py b/dandi/cli/command.py → lincbrain/cli/command.py
diff --git a/dandi/cli/formatter.py → lincbrain/cli/formatter.py b/dandi/cli/formatter.py → lincbrain/cli/formatter.py
diff --git a/dandi/cli/tests/__init__.py → lincbrain/cli/tests/__init__.py b/dandi/cli/tests/__init__.py → lincbrain/cli/tests/__init__.py
diff --git a/...ata/update_dandiset_from_doi/biorxiv.json → ...ata/update_dandiset_from_doi/biorxiv.json b/...ata/update_dandiset_from_doi/biorxiv.json → ...ata/update_dandiset_from_doi/biorxiv.json
diff --git a/...update_dandiset_from_doi/biorxiv.vcr.yaml → ...update_dandiset_from_doi/biorxiv.vcr.yaml b/...update_dandiset_from_doi/biorxiv.vcr.yaml → ...update_dandiset_from_doi/biorxiv.vcr.yaml
diff --git a/.../data/update_dandiset_from_doi/elife.json → .../data/update_dandiset_from_doi/elife.json b/.../data/update_dandiset_from_doi/elife.json → .../data/update_dandiset_from_doi/elife.json
diff --git a/...a/update_dandiset_from_doi/elife.vcr.yaml → ...a/update_dandiset_from_doi/elife.vcr.yaml b/...a/update_dandiset_from_doi/elife.vcr.yaml → ...a/update_dandiset_from_doi/elife.vcr.yaml
diff --git a/...a/update_dandiset_from_doi/jneurosci.json → ...a/update_dandiset_from_doi/jneurosci.json b/...a/update_dandiset_from_doi/jneurosci.json → ...a/update_dandiset_from_doi/jneurosci.json
diff --git a/...date_dandiset_from_doi/jneurosci.vcr.yaml → ...date_dandiset_from_doi/jneurosci.vcr.yaml b/...date_dandiset_from_doi/jneurosci.vcr.yaml → ...date_dandiset_from_doi/jneurosci.vcr.yaml
diff --git a/...data/update_dandiset_from_doi/nature.json → ...data/update_dandiset_from_doi/nature.json b/...data/update_dandiset_from_doi/nature.json → ...data/update_dandiset_from_doi/nature.json
diff --git a/.../update_dandiset_from_doi/nature.vcr.yaml → .../update_dandiset_from_doi/nature.vcr.yaml b/.../update_dandiset_from_doi/nature.vcr.yaml → .../update_dandiset_from_doi/nature.vcr.yaml
diff --git a/...data/update_dandiset_from_doi/neuron.json → ...data/update_dandiset_from_doi/neuron.json b/...data/update_dandiset_from_doi/neuron.json → ...data/update_dandiset_from_doi/neuron.json
diff --git a/.../update_dandiset_from_doi/neuron.vcr.yaml → .../update_dandiset_from_doi/neuron.vcr.yaml b/.../update_dandiset_from_doi/neuron.vcr.yaml → .../update_dandiset_from_doi/neuron.vcr.yaml
diff --git a/dandi/cli/tests/test_cmd_ls.py → lincbrain/cli/tests/test_cmd_ls.py b/dandi/cli/tests/test_cmd_ls.py → lincbrain/cli/tests/test_cmd_ls.py
diff --git a/dandi/cli/tests/test_cmd_validate.py → lincbrain/cli/tests/test_cmd_validate.py b/dandi/cli/tests/test_cmd_validate.py → lincbrain/cli/tests/test_cmd_validate.py
diff --git a/dandi/cli/tests/test_command.py → lincbrain/cli/tests/test_command.py b/dandi/cli/tests/test_command.py → lincbrain/cli/tests/test_command.py
diff --git a/dandi/cli/tests/test_digest.py → lincbrain/cli/tests/test_digest.py b/dandi/cli/tests/test_digest.py → lincbrain/cli/tests/test_digest.py
diff --git a/dandi/cli/tests/test_download.py → lincbrain/cli/tests/test_download.py b/dandi/cli/tests/test_download.py → lincbrain/cli/tests/test_download.py
diff --git a/dandi/cli/tests/test_formatter.py → lincbrain/cli/tests/test_formatter.py b/dandi/cli/tests/test_formatter.py → lincbrain/cli/tests/test_formatter.py
diff --git a/dandi/cli/tests/test_instances.py → lincbrain/cli/tests/test_instances.py b/dandi/cli/tests/test_instances.py → lincbrain/cli/tests/test_instances.py
diff --git a/dandi/cli/tests/test_move.py → lincbrain/cli/tests/test_move.py b/dandi/cli/tests/test_move.py → lincbrain/cli/tests/test_move.py
diff --git a/dandi/cli/tests/test_service_scripts.py → lincbrain/cli/tests/test_service_scripts.py b/dandi/cli/tests/test_service_scripts.py → lincbrain/cli/tests/test_service_scripts.py
diff --git a/dandi/cli/tests/test_shell_completion.py → lincbrain/cli/tests/test_shell_completion.py b/dandi/cli/tests/test_shell_completion.py → lincbrain/cli/tests/test_shell_completion.py
diff --git a/dandi/conftest.py → lincbrain/conftest.py b/dandi/conftest.py → lincbrain/conftest.py
diff --git a/dandi/consts.py → lincbrain/consts.py b/dandi/consts.py → lincbrain/consts.py
diff --git a/dandi/dandiapi.py → lincbrain/dandiapi.py b/dandi/dandiapi.py → lincbrain/dandiapi.py
diff --git a/dandi/dandiarchive.py → lincbrain/dandiarchive.py b/dandi/dandiarchive.py → lincbrain/dandiarchive.py
diff --git a/dandi/dandiset.py → lincbrain/dandiset.py b/dandi/dandiset.py → lincbrain/dandiset.py
diff --git a/dandi/delete.py → lincbrain/delete.py b/dandi/delete.py → lincbrain/delete.py
diff --git a/dandi/download.py → lincbrain/download.py b/dandi/download.py → lincbrain/download.py
diff --git a/dandi/due.py → lincbrain/due.py b/dandi/due.py → lincbrain/due.py
diff --git a/dandi/exceptions.py → lincbrain/exceptions.py b/dandi/exceptions.py → lincbrain/exceptions.py
diff --git a/dandi/files/__init__.py → lincbrain/files/__init__.py b/dandi/files/__init__.py → lincbrain/files/__init__.py
diff --git a/dandi/files/_private.py → lincbrain/files/_private.py b/dandi/files/_private.py → lincbrain/files/_private.py
diff --git a/dandi/files/bases.py → lincbrain/files/bases.py b/dandi/files/bases.py → lincbrain/files/bases.py
diff --git a/dandi/files/bids.py → lincbrain/files/bids.py b/dandi/files/bids.py → lincbrain/files/bids.py
diff --git a/dandi/files/zarr.py → lincbrain/files/zarr.py b/dandi/files/zarr.py → lincbrain/files/zarr.py
diff --git a/dandi/keyring.py → lincbrain/keyring.py b/dandi/keyring.py → lincbrain/keyring.py
diff --git a/dandi/metadata/__init__.py → lincbrain/metadata/__init__.py b/dandi/metadata/__init__.py → lincbrain/metadata/__init__.py
diff --git a/dandi/metadata/core.py → lincbrain/metadata/core.py b/dandi/metadata/core.py → lincbrain/metadata/core.py
diff --git a/dandi/metadata/nwb.py → lincbrain/metadata/nwb.py b/dandi/metadata/nwb.py → lincbrain/metadata/nwb.py
diff --git a/dandi/metadata/util.py → lincbrain/metadata/util.py b/dandi/metadata/util.py → lincbrain/metadata/util.py
diff --git a/dandi/misctypes.py → lincbrain/misctypes.py b/dandi/misctypes.py → lincbrain/misctypes.py
diff --git a/dandi/move.py → lincbrain/move.py b/dandi/move.py → lincbrain/move.py
diff --git a/dandi/organize.py → lincbrain/organize.py b/dandi/organize.py → lincbrain/organize.py
diff --git a/dandi/pynwb_utils.py → lincbrain/pynwb_utils.py b/dandi/pynwb_utils.py → lincbrain/pynwb_utils.py
diff --git a/dandi/support/__init__.py → lincbrain/support/__init__.py b/dandi/support/__init__.py → lincbrain/support/__init__.py
diff --git a/dandi/support/digests.py → lincbrain/support/digests.py b/dandi/support/digests.py → lincbrain/support/digests.py
diff --git a/dandi/support/iterators.py → lincbrain/support/iterators.py b/dandi/support/iterators.py → lincbrain/support/iterators.py
diff --git a/dandi/support/pyout.py → lincbrain/support/pyout.py b/dandi/support/pyout.py → lincbrain/support/pyout.py
diff --git a/dandi/support/tests/__init__.py → lincbrain/support/tests/__init__.py b/dandi/support/tests/__init__.py → lincbrain/support/tests/__init__.py
diff --git a/dandi/support/tests/test_digests.py → lincbrain/support/tests/test_digests.py b/dandi/support/tests/test_digests.py → lincbrain/support/tests/test_digests.py
diff --git a/dandi/support/tests/test_iterators.py → lincbrain/support/tests/test_iterators.py b/dandi/support/tests/test_iterators.py → lincbrain/support/tests/test_iterators.py
diff --git a/dandi/support/threaded_walk.py → lincbrain/support/threaded_walk.py b/dandi/support/threaded_walk.py → lincbrain/support/threaded_walk.py
diff --git a/dandi/tests/__init__.py → lincbrain/tests/__init__.py b/dandi/tests/__init__.py → lincbrain/tests/__init__.py
diff --git a/...ta/dandiarchive-docker/docker-compose.yml → ...ta/dandiarchive-docker/docker-compose.yml b/...ta/dandiarchive-docker/docker-compose.yml → ...ta/dandiarchive-docker/docker-compose.yml
diff --git a/...ata/metadata/dandimeta_migration.new.json → ...ata/metadata/dandimeta_migration.new.json b/...ata/metadata/dandimeta_migration.new.json → ...ata/metadata/dandimeta_migration.new.json
diff --git a/...i/tests/data/metadata/metadata2asset.json → ...n/tests/data/metadata/metadata2asset.json b/...i/tests/data/metadata/metadata2asset.json → ...n/tests/data/metadata/metadata2asset.json
diff --git a/...tests/data/metadata/metadata2asset_3.json → ...tests/data/metadata/metadata2asset_3.json b/...tests/data/metadata/metadata2asset_3.json → ...tests/data/metadata/metadata2asset_3.json
diff --git a/...ata/metadata/metadata2asset_cellline.json → ...ata/metadata/metadata2asset_cellline.json b/...ata/metadata/metadata2asset_cellline.json → ...ata/metadata/metadata2asset_cellline.json
diff --git a/...data/metadata/metadata2asset_simple1.json → ...data/metadata/metadata2asset_simple1.json b/...data/metadata/metadata2asset_simple1.json → ...data/metadata/metadata2asset_simple1.json
diff --git a/dandi/tests/fixtures.py → lincbrain/tests/fixtures.py b/dandi/tests/fixtures.py → lincbrain/tests/fixtures.py
diff --git a/dandi/tests/skip.py → lincbrain/tests/skip.py b/dandi/tests/skip.py → lincbrain/tests/skip.py
diff --git a/dandi/tests/test_dandiapi.py → lincbrain/tests/test_dandiapi.py b/dandi/tests/test_dandiapi.py → lincbrain/tests/test_dandiapi.py
diff --git a/dandi/tests/test_dandiarchive.py → lincbrain/tests/test_dandiarchive.py b/dandi/tests/test_dandiarchive.py → lincbrain/tests/test_dandiarchive.py
diff --git a/dandi/tests/test_dandiset.py → lincbrain/tests/test_dandiset.py b/dandi/tests/test_dandiset.py → lincbrain/tests/test_dandiset.py
diff --git a/dandi/tests/test_delete.py → lincbrain/tests/test_delete.py b/dandi/tests/test_delete.py → lincbrain/tests/test_delete.py
diff --git a/dandi/tests/test_download.py → lincbrain/tests/test_download.py b/dandi/tests/test_download.py → lincbrain/tests/test_download.py
diff --git a/dandi/tests/test_files.py → lincbrain/tests/test_files.py b/dandi/tests/test_files.py → lincbrain/tests/test_files.py
diff --git a/dandi/tests/test_fixtures.py → lincbrain/tests/test_fixtures.py b/dandi/tests/test_fixtures.py → lincbrain/tests/test_fixtures.py
diff --git a/dandi/tests/test_helpers.py → lincbrain/tests/test_helpers.py b/dandi/tests/test_helpers.py → lincbrain/tests/test_helpers.py
diff --git a/dandi/tests/test_keyring.py → lincbrain/tests/test_keyring.py b/dandi/tests/test_keyring.py → lincbrain/tests/test_keyring.py
diff --git a/dandi/tests/test_metadata.py → lincbrain/tests/test_metadata.py b/dandi/tests/test_metadata.py → lincbrain/tests/test_metadata.py
diff --git a/dandi/tests/test_move.py → lincbrain/tests/test_move.py b/dandi/tests/test_move.py → lincbrain/tests/test_move.py
diff --git a/dandi/tests/test_organize.py → lincbrain/tests/test_organize.py b/dandi/tests/test_organize.py → lincbrain/tests/test_organize.py
diff --git a/dandi/tests/test_pynwb_utils.py → lincbrain/tests/test_pynwb_utils.py b/dandi/tests/test_pynwb_utils.py → lincbrain/tests/test_pynwb_utils.py
diff --git a/dandi/tests/test_upload.py → lincbrain/tests/test_upload.py b/dandi/tests/test_upload.py → lincbrain/tests/test_upload.py
diff --git a/dandi/tests/test_utils.py → lincbrain/tests/test_utils.py b/dandi/tests/test_utils.py → lincbrain/tests/test_utils.py
diff --git a/dandi/tests/test_validate.py → lincbrain/tests/test_validate.py b/dandi/tests/test_validate.py → lincbrain/tests/test_validate.py
diff --git a/dandi/upload.py → lincbrain/upload.py b/dandi/upload.py → lincbrain/upload.py
diff --git a/dandi/utils.py → lincbrain/utils.py b/dandi/utils.py → lincbrain/utils.py
diff --git a/dandi/validate.py → lincbrain/validate.py b/dandi/validate.py → lincbrain/validate.py
diff --git a/dandi/validate_types.py → lincbrain/validate_types.py b/dandi/validate_types.py → lincbrain/validate_types.py
diff --git a/setup.cfg b/setup.cfg
@@ -61,7 +61,7 @@ packages = find_namespace:
 include_package_data = True
 
 [options.packages.find]
-include = dandi*
+include = lincbrain*
 
 [options.extras_require]
 # I bet will come handy
@@ -101,7 +101,7 @@ all =
 
 [options.entry_points]
 console_scripts =
-    lincbrain=dandi.cli.command:main
+    lincbrain=lincbrain.cli.command:main
 
 [flake8]
 max-line-length = 100
@@ -113,8 +113,8 @@ extend-exclude =
 [versioneer]
 VCS = git
 style = pep440
-versionfile_source = dandi/_version.py
-versionfile_build = dandi/_version.py
+versionfile_source = lincbrain/_version.py
+versionfile_build = lincbrain/_version.py
 tag_prefix =
 parentdir_prefix =
 

diff --git a/setup.py b/setup.py
@@ -41,6 +41,6 @@
 if __name__ == "__main__":
     setup(
         name="lincbrain",
-        version="0.6.0",
+        version="0.9.0",
         cmdclass={},
     )