Submodule

[ivirshup]

Making a doc update for scanpy 1.10. Includes some changes for this to better support being a gitsubmodule, though also makes a minor updates to docs.

see https://github.com/scverse/scanpy/pull/2901

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flying-sheep commented on 2024-03-22T10:33:26Z ----------------------------------------------------------------

Line #4.    )  # "MT-" for human, "Mt-" for mouse

please move the comment above the line for better formatting

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flying-sheep commented on 2024-03-22T10:33:26Z ----------------------------------------------------------------

Is there a citation for the “permissive filtering” insight? If everything is explained in luecken2021, maybe mention that.

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flying-sheep commented on 2024-03-22T10:33:27Z ----------------------------------------------------------------

Looks like quite some overplotting. Maybe mention that this is not an ideal representation of the density of the samples?

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flying-sheep commented on 2024-03-22T10:33:28Z ----------------------------------------------------------------

We throw a deprecation warning when not using it, right? Maybe mention that scanpy recommends using it.

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flying-sheep commented on 2024-03-22T10:33:29Z ----------------------------------------------------------------

Why cluster before this?

ivirshup commented on 2024-03-22T21:25:14Z ----------------------------------------------------------------

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

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flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

here too: move the comments above their dict entries to give them a chance to go on one line. (make sure you re-format with the last comma per list removed so the formatter doesn’t keep it on multiple lines)

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flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

This part is confusing. You redefine the cluster3_genes variable, the names in this text cell don’t correspond to the names the code emits, please check this part again

review-notebook-app[bot] commented 8 months ago

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flying-sheep commented on 2024-03-22T10:33:31Z ----------------------------------------------------------------

this is not a violin plot as advertised

ivirshup commented 8 months ago

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

---

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ivirshup commented 8 months ago

I believe I've addressed everything and want to get moving on the release. Open follow up issues for anything else.

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

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flying-sheep commented on 2024-03-22T10:33:26Z ----------------------------------------------------------------

Is there a citation for the “permissive filtering” insight? If everything is explained in luecken2021, maybe mention that.

review-notebook-app[bot] commented 8 months ago

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flying-sheep commented on 2024-03-22T10:33:27Z ----------------------------------------------------------------

Looks like quite some overplotting. Maybe mention that this is not an ideal representation of the density of the samples?

review-notebook-app[bot] commented 8 months ago

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flying-sheep commented on 2024-03-22T10:33:28Z ----------------------------------------------------------------

We throw a deprecation warning when not using it, right? Maybe mention that scanpy recommends using it.

review-notebook-app[bot] commented 8 months ago

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flying-sheep commented on 2024-03-22T10:33:29Z ----------------------------------------------------------------

Why cluster before this?

ivirshup commented on 2024-03-22T21:25:14Z ----------------------------------------------------------------

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

review-notebook-app[bot] commented 8 months ago

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flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

here too: move the comments above their dict entries to give them a chance to go on one line. (make sure you re-format with the last comma per list removed so the formatter doesn’t keep it on multiple lines)

review-notebook-app[bot] commented 8 months ago

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flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

This part is confusing. You redefine the cluster3_genes variable, the names in this text cell don’t correspond to the names the code emits, please check this part again

review-notebook-app[bot] commented 8 months ago

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flying-sheep commented on 2024-03-22T10:33:31Z ----------------------------------------------------------------

this is not a violin plot as advertised

ivirshup commented 8 months ago

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

---

View entire conversation on ReviewNB

ivirshup commented 8 months ago

I believe I've addressed everything and want to get moving on the release. Open follow up issues for anything else.

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[review-notebook-app[bot]]

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:27Z ----------------------------------------------------------------

Looks like quite some overplotting. Maybe mention that this is not an ideal representation of the density of the samples?

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:28Z ----------------------------------------------------------------

We throw a deprecation warning when not using it, right? Maybe mention that scanpy recommends using it.

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:29Z ----------------------------------------------------------------

Why cluster before this?

ivirshup commented on 2024-03-22T21:25:14Z ----------------------------------------------------------------

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

here too: move the comments above their dict entries to give them a chance to go on one line. (make sure you re-format with the last comma per list removed so the formatter doesn’t keep it on multiple lines)

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

This part is confusing. You redefine the cluster3_genes variable, the names in this text cell don’t correspond to the names the code emits, please check this part again

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:31Z ----------------------------------------------------------------

this is not a violin plot as advertised

ivirshup commented 8 months ago

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

---

View entire conversation on ReviewNB

ivirshup commented 8 months ago

I believe I've addressed everything and want to get moving on the release. Open follow up issues for anything else.

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[review-notebook-app[bot]]

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:28Z ----------------------------------------------------------------

We throw a deprecation warning when not using it, right? Maybe mention that scanpy recommends using it.

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:29Z ----------------------------------------------------------------

Why cluster before this?

ivirshup commented on 2024-03-22T21:25:14Z ----------------------------------------------------------------

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

here too: move the comments above their dict entries to give them a chance to go on one line. (make sure you re-format with the last comma per list removed so the formatter doesn’t keep it on multiple lines)

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

This part is confusing. You redefine the cluster3_genes variable, the names in this text cell don’t correspond to the names the code emits, please check this part again

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:31Z ----------------------------------------------------------------

this is not a violin plot as advertised

ivirshup commented 8 months ago

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

---

View entire conversation on ReviewNB

ivirshup commented 8 months ago

I believe I've addressed everything and want to get moving on the release. Open follow up issues for anything else.

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[review-notebook-app[bot]]

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:29Z ----------------------------------------------------------------

Why cluster before this?

ivirshup commented on 2024-03-22T21:25:14Z ----------------------------------------------------------------

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

here too: move the comments above their dict entries to give them a chance to go on one line. (make sure you re-format with the last comma per list removed so the formatter doesn’t keep it on multiple lines)

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

This part is confusing. You redefine the cluster3_genes variable, the names in this text cell don’t correspond to the names the code emits, please check this part again

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:31Z ----------------------------------------------------------------

this is not a violin plot as advertised

ivirshup commented 8 months ago

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

---

View entire conversation on ReviewNB

ivirshup commented 8 months ago

I believe I've addressed everything and want to get moving on the release. Open follow up issues for anything else.

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[review-notebook-app[bot]]

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

here too: move the comments above their dict entries to give them a chance to go on one line. (make sure you re-format with the last comma per list removed so the formatter doesn’t keep it on multiple lines)

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

This part is confusing. You redefine the cluster3_genes variable, the names in this text cell don’t correspond to the names the code emits, please check this part again

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:31Z ----------------------------------------------------------------

this is not a violin plot as advertised

ivirshup commented 8 months ago

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

---

View entire conversation on ReviewNB

ivirshup commented 8 months ago

I believe I've addressed everything and want to get moving on the release. Open follow up issues for anything else.

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[review-notebook-app[bot]]

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:30Z ----------------------------------------------------------------

This part is confusing. You redefine the cluster3_genes variable, the names in this text cell don’t correspond to the names the code emits, please check this part again

review-notebook-app[bot] commented 8 months ago

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:31Z ----------------------------------------------------------------

this is not a violin plot as advertised

ivirshup commented 8 months ago

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

---

View entire conversation on ReviewNB

ivirshup commented 8 months ago

I believe I've addressed everything and want to get moving on the release. Open follow up issues for anything else.

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[review-notebook-app[bot]]

View / edit / reply to this conversation on ReviewNB

flying-sheep commented on 2024-03-22T10:33:31Z ----------------------------------------------------------------

this is not a violin plot as advertised

ivirshup commented 8 months ago

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

---

View entire conversation on ReviewNB

ivirshup commented 8 months ago

I believe I've addressed everything and want to get moving on the release. Open follow up issues for anything else.

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[ivirshup]

Largely because I don't want to vary too much from the main notebook over on scverse-tutorials.

Tbh we could probably just remove this block, and suggest that the process should be iterative and maybe clusters should be removed.

---

View entire conversation on ReviewNB

[ivirshup]

I believe I've addressed everything and want to get moving on the release. Open follow up issues for anything else.