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Merged
merged 22 commits into from
Jul 12, 2022
Merged

Standard integration tests, PEP8, docker adjustments #23

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dcb062a
WIP PEP8
CBroz1 May 2, 2022
2f842b2
WIP Draft integration tests
CBroz1 May 4, 2022
bbfe140
WIP standard pytests. missing element-event. passed CLI, need docker …
CBroz1 May 4, 2022
c143548
WIP docker edits
CBroz1 May 5, 2022
7d4f879
minor docker changes
CBroz1 May 6, 2022
0cfdcf3
Revised docker from @iamamutt
CBroz1 May 13, 2022
90d0d74
Apply suggestions from code review
CBroz1 May 16, 2022
c77ac0c
WIP. Replace with dj image. TLS config statement
CBroz1 May 17, 2022
39d252d
Docker success *if detatched*
CBroz1 May 23, 2022
6a66ec4
Add contact info to Code of Conduct
CBroz1 Jun 17, 2022
a875dca
Remove order constraints in test_pipeline_generation
CBroz1 Jun 23, 2022
a777f34
WIP: Apply suggestions 1
CBroz1 Jul 8, 2022
c34d325
WIP: Apply suggestions 2
CBroz1 Jul 8, 2022
7e41a3a
WIP: Apply suggestions 3. All except Docker
CBroz1 Jul 8, 2022
217a84d
Revert dockerfile arg; adjust 05-explore
CBroz1 Jul 8, 2022
d7165ac
Apply suggestions from code review
CBroz1 Jul 12, 2022
8435df2
WIP. See details. Jupysync, verbose context, abc.Seq, etc.
CBroz1 Jul 12, 2022
b1e45a2
WIP: verbosity if to oneliner
CBroz1 Jul 12, 2022
68b04ed
Version bump
CBroz1 Jul 12, 2022
6fc72ee
Notebook fix black'd issues. Docker compose vol map
CBroz1 Jul 12, 2022
fd89eba
Revise notebook 02 - formatting issues
CBroz1 Jul 12, 2022
50fcc20
Revert nb 05
CBroz1 Jul 12, 2022
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WIP. See details. Jupysync, verbose context, abc.Seq, etc. 
notebooks: Run Jupytext sync
tests/__init__ : set conditional verbose context in constants, remove numpy
workflow_mini/paths: list->abc.Sequence
docker/docker-compose-test: uncomment volumes
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@CBroz1
CBroz1 committed Jul 12, 2022
commit 8435df28ccc4e1a5b4572f1462c242137e30cd04
4 changes: 2 additions & 2 deletions docker/docker-compose-test.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -62,5 +62,5 @@ networks:
miniscope:
name: workflow-miniscope-network

# volumes:
# mysql-miniscope:
volumes:
mysql-miniscope:
Comment on lines +67 to +68
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@kabilar kabilar Jul 5, 2022

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Is this required since the above code is commented out?

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@CBroz1 CBroz1 Jul 8, 2022

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Hi @iamamutt - Could you remind me why volumes is here? I see it in the copy you drafted prior to this PR. Does networks not provide what we need on it's own?

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@iamamutt iamamutt Jul 8, 2022

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@CBroz1 That was there to map the data from the mysql database to a docker volume instead of bind mounting to the local filesystem. If you don't need access to the database data at all, you can delete the volumes section at the bottom, +72 to +73, and also it's mention at lines +19 to +20.

If you want a bind mounted volume, change - mysql-miniscope:/var/lib/mysql to - path/to/some/data/dir:/var/lib/mysql, and you can delete the volumes section at the end of the file.

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@CBroz1 CBroz1 Jul 8, 2022

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That makes sense. Thanks @iamamutt!

15 changes: 10 additions & 5 deletions notebooks/02-workflow-structure-optional.ipynb
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Expand Up @@ -51,6 +51,7 @@
"execution_count": null,
"id": "693929a9",
"metadata": {
"lines_to_next_cell": 2,
"title": "Each module contains a schema object that enables interaction with the schema in the database."
},
"outputs": [],
Expand All @@ -72,6 +73,7 @@
"execution_count": null,
"id": "d0ee126a",
"metadata": {
"lines_to_next_cell": 2,
"title": "The table classes in the module corresponds to a table in the schema in the database."
},
"outputs": [],
Expand All @@ -96,9 +98,9 @@
"title": "The first time importing the modules, empty schemas and tables will be created in the database."
},
"source": [
"# + By importing the modules for the first time, the schemas and tables will be created inside the database.\n",
"# # + By importing the modules for the first time, the schemas and tables will be created inside the database.\n",
"\n",
"# + Once created, importing modules will not create schemas and tables again, but the existing schemas/tables can be accessed and manipulated by the modules."
"# # + Once created, importing modules will not create schemas and tables again, but the existing schemas/tables can be accessed and manipulated by the modules."
]
},
{
Expand All @@ -110,7 +112,7 @@
"source": [
"## DataJoint tools to explore schemas and tables\n",
"\n",
"# + `dj.list_schemas()`: list all schemas a user has access to in the current database"
"# # + `dj.list_schemas()`: list all schemas a user has access to in the current database"
]
},
{
Expand All @@ -129,6 +131,7 @@
"execution_count": null,
"id": "687dbcb3",
"metadata": {
"lines_to_next_cell": 2,
"title": "`dj.Diagram()`: plot tables and dependencies in a schema."
},
"outputs": [],
Expand Down Expand Up @@ -214,7 +217,7 @@
"title": "`heading`:"
},
"source": [
"# + `describe()`: show table definition with foreign key references."
"# # + `describe()`: show table definition with foreign key references."
]
},
{
Expand All @@ -231,6 +234,7 @@
"execution_count": null,
"id": "08837864",
"metadata": {
"lines_to_next_cell": 2,
"title": "`heading`: show attribute definitions regardless of foreign key references"
},
"outputs": [],
Expand All @@ -255,7 +259,7 @@
"source": [
"# DataJoint Elements installed in `workflow-miniscope`\n",
"\n",
"# + [`lab`](https://github.com/datajoint/element-lab): lab management related information, such as Lab, User, Project, Protocol, Source."
"# # + [`lab`](https://github.com/datajoint/element-lab): lab management related information, such as Lab, User, Project, Protocol, Source."
]
},
{
Expand Down Expand Up @@ -318,6 +322,7 @@
"execution_count": null,
"id": "dc175fed",
"metadata": {
"lines_to_next_cell": 2,
"title": "[`miniscope`](https://github.com/datajoint/element-miniscope): miniscope raw recording and processed data"
},
"outputs": [],
Expand Down
21 changes: 0 additions & 21 deletions notebooks/03-process.ipynb
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Expand Up @@ -843,27 +843,6 @@
" session_datetime='2021-01-01 00:00:01')"
]
},
{
"cell_type": "code",
"execution_count": 50,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['`u24_miniscope`.`_recording_info__file`',\n",
" '`u24_miniscope`.`processing_task`']"
]
},
"execution_count": 50,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"miniscope.RecordingInfo.children(as_objects=False)"
]
},
{
"cell_type": "code",
"execution_count": 26,
Expand Down
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