update data_container example to pymc 5.6

[jessegrabowski]

Update how_to/data_container to PyMC 5.6

Related to #333

The data container notebook is out of date. It uses PyMC3, and uses several APIs that are no longer needed/suggested/supported. Most prominent is using pm.Data instead of specifying pm.MutableData, but other small updates include:

• Remove return_inferencedata=True from pm.sample
• It is no longer necessary to make a custom group with az.from_pymc to add a predictions group; users should instead use the predictions=True flag in pm.sample_posterior_predictive
• The same is also true about manually extending idata to include a posterior_predictive group; users should pass extend_idata=True instead
• A referenced error that didn't allow setting a single observation has since been fixed

I also added a small explanation about the difference between pm.ConstantData and how to set mutable coords using model.add_coord. There might be a better way to do that last one.

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:books: Documentation preview :books:: https://pymc-examples--559.org.readthedocs.build/en/559/

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[jessegrabowski]

Just saw #527, I didn't even know this feature existed. I'll update this notebook to use it in the final example.

[OriolAbril]

Thanks! This is great, we get questions about this quite often

[jessegrabowski]

I refactored the last baby weight example to:

1. Remove unicode greek names (following the examples style guide)
2. Include both mutable and constant coords, to highlight the difference

I think (2) is important, since it's not really a documented feature anywhere yet.

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twiecki commented on 2023-07-12T09:26:25Z ----------------------------------------------------------------

Should we just rename this to Using Data containers?

jessegrabowski commented on 2023-07-12T09:46:55Z ----------------------------------------------------------------

I like that better, since users don't need to know what a "shared variable" is to use the data containers API

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twiecki commented on 2023-07-12T09:26:26Z ----------------------------------------------------------------

*allow you to

Maybe also mention why anyone would want to use ConstantData (performance).

Also, I think that pm.Data also allows specification of dims, no? The only reason we have Data, MutableData, and ConstantData is historical and I think we should say that best practice is to use MutableData and ConstantData and only mention Data as a side-note.

jessegrabowski commented on 2023-07-12T09:44:57Z ----------------------------------------------------------------

I was thinking it would be nice to change one of the examples to use ConstantData, so that there's one usage for both. Maybe the first example. Then we could change around some headings (to point out which container is being used in which section, and why)?

A short passage at the beginning could be added, like "In past versions of PyMC, data was added to a model using pm.Data. While this is still possible for backwards-comparability reasons, the current best practice is to use either pm.MutableData or pm.ConstantData,depending on your needs. This notebook will demonstrate how each of these data containers are used, and when they are appropriate".

twiecki commented on 2023-07-13T10:20:53Z ----------------------------------------------------------------

Yes, I think that's perfect.

jessegrabowski commented on 2023-07-13T10:59:44Z ----------------------------------------------------------------

I tried adding some details about each of the containers and give an example for each, let me know if it falls short of the mark.

review-notebook-app[bot] commented 12 months ago

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twiecki commented on 2023-07-12T09:26:27Z ----------------------------------------------------------------

size is internal API, either use shape, or, better yet, also a dummy-dim.

jessegrabowski commented on 2023-07-12T09:51:08Z ----------------------------------------------------------------

What do you mean by a dummy dim?

twiecki commented on 2023-07-13T10:20:20Z ----------------------------------------------------------------

Oh, I see what you're doing here now. I think it should just be shape though.

jessegrabowski commented 12 months ago

I was thinking it would be nice to change one of the examples to use ConstantData, so that there's one usage for both. Maybe the first example. Then we could change around some headings (to point out which container is being used in which section, and why)?

A short passage at the beginning could be added, like "In past versions of PyMC, data was added to a model using pm.Data. While this is still possible for backwards-comparability reasons, the current best practice is to use either pm.MutableData or pm.ConstantData,depending on your needs. This notebook will demonstrate how each of these data containers are used, and when they are appropriate".

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jessegrabowski commented 12 months ago

I like that better, since users don't need to know what a "shared variable" is to use the data containers API

---

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jessegrabowski commented 12 months ago

What do you mean by a dummy dim?

---

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twiecki commented 12 months ago

Oh, I see what you're doing here now. I think it should just be shape though.

---

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twiecki commented 12 months ago

Yes, I think that's perfect.

---

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jessegrabowski commented 12 months ago

I tried adding some details about each of the containers and give an example for each, let me know if it falls short of the mark.

---

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twiecki commented on 2023-07-12T09:26:26Z ----------------------------------------------------------------

*allow you to

Maybe also mention why anyone would want to use ConstantData (performance).

Also, I think that pm.Data also allows specification of dims, no? The only reason we have Data, MutableData, and ConstantData is historical and I think we should say that best practice is to use MutableData and ConstantData and only mention Data as a side-note.

jessegrabowski commented on 2023-07-12T09:44:57Z ----------------------------------------------------------------

I was thinking it would be nice to change one of the examples to use ConstantData, so that there's one usage for both. Maybe the first example. Then we could change around some headings (to point out which container is being used in which section, and why)?

A short passage at the beginning could be added, like "In past versions of PyMC, data was added to a model using pm.Data. While this is still possible for backwards-comparability reasons, the current best practice is to use either pm.MutableData or pm.ConstantData,depending on your needs. This notebook will demonstrate how each of these data containers are used, and when they are appropriate".

twiecki commented on 2023-07-13T10:20:53Z ----------------------------------------------------------------

Yes, I think that's perfect.

jessegrabowski commented on 2023-07-13T10:59:44Z ----------------------------------------------------------------

I tried adding some details about each of the containers and give an example for each, let me know if it falls short of the mark.

review-notebook-app[bot] commented 12 months ago

View / edit / reply to this conversation on ReviewNB

twiecki commented on 2023-07-12T09:26:27Z ----------------------------------------------------------------

size is internal API, either use shape, or, better yet, also a dummy-dim.

jessegrabowski commented on 2023-07-12T09:51:08Z ----------------------------------------------------------------

What do you mean by a dummy dim?

twiecki commented on 2023-07-13T10:20:20Z ----------------------------------------------------------------

Oh, I see what you're doing here now. I think it should just be shape though.

jessegrabowski commented 12 months ago

I was thinking it would be nice to change one of the examples to use ConstantData, so that there's one usage for both. Maybe the first example. Then we could change around some headings (to point out which container is being used in which section, and why)?

A short passage at the beginning could be added, like "In past versions of PyMC, data was added to a model using pm.Data. While this is still possible for backwards-comparability reasons, the current best practice is to use either pm.MutableData or pm.ConstantData,depending on your needs. This notebook will demonstrate how each of these data containers are used, and when they are appropriate".

---

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jessegrabowski commented 12 months ago

I like that better, since users don't need to know what a "shared variable" is to use the data containers API

---

View entire conversation on ReviewNB

jessegrabowski commented 12 months ago

What do you mean by a dummy dim?

---

View entire conversation on ReviewNB

twiecki commented 12 months ago

Oh, I see what you're doing here now. I think it should just be shape though.

---

View entire conversation on ReviewNB

twiecki commented 12 months ago

Yes, I think that's perfect.

---

View entire conversation on ReviewNB

jessegrabowski commented 12 months ago

I tried adding some details about each of the containers and give an example for each, let me know if it falls short of the mark.

---

View entire conversation on ReviewNB

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

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twiecki commented on 2023-07-12T09:26:27Z ----------------------------------------------------------------

size is internal API, either use shape, or, better yet, also a dummy-dim.

jessegrabowski commented on 2023-07-12T09:51:08Z ----------------------------------------------------------------

What do you mean by a dummy dim?

twiecki commented on 2023-07-13T10:20:20Z ----------------------------------------------------------------

Oh, I see what you're doing here now. I think it should just be shape though.

jessegrabowski commented 12 months ago

I was thinking it would be nice to change one of the examples to use ConstantData, so that there's one usage for both. Maybe the first example. Then we could change around some headings (to point out which container is being used in which section, and why)?

A short passage at the beginning could be added, like "In past versions of PyMC, data was added to a model using pm.Data. While this is still possible for backwards-comparability reasons, the current best practice is to use either pm.MutableData or pm.ConstantData,depending on your needs. This notebook will demonstrate how each of these data containers are used, and when they are appropriate".

---

View entire conversation on ReviewNB

jessegrabowski commented 12 months ago

I like that better, since users don't need to know what a "shared variable" is to use the data containers API

---

View entire conversation on ReviewNB

jessegrabowski commented 12 months ago

What do you mean by a dummy dim?

---

View entire conversation on ReviewNB

twiecki commented 12 months ago

Oh, I see what you're doing here now. I think it should just be shape though.

---

View entire conversation on ReviewNB

twiecki commented 12 months ago

Yes, I think that's perfect.

---

View entire conversation on ReviewNB

jessegrabowski commented 12 months ago

I tried adding some details about each of the containers and give an example for each, let me know if it falls short of the mark.

---

View entire conversation on ReviewNB

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

[jessegrabowski]

I was thinking it would be nice to change one of the examples to use ConstantData, so that there's one usage for both. Maybe the first example. Then we could change around some headings (to point out which container is being used in which section, and why)?

A short passage at the beginning could be added, like "In past versions of PyMC, data was added to a model using pm.Data. While this is still possible for backwards-comparability reasons, the current best practice is to use either pm.MutableData or pm.ConstantData,depending on your needs. This notebook will demonstrate how each of these data containers are used, and when they are appropriate".

---

View entire conversation on ReviewNB

[jessegrabowski]

I like that better, since users don't need to know what a "shared variable" is to use the data containers API

---

View entire conversation on ReviewNB

[jessegrabowski]

What do you mean by a dummy dim?

---

View entire conversation on ReviewNB

[twiecki]

Oh, I see what you're doing here now. I think it should just be shape though.

---

View entire conversation on ReviewNB

[twiecki]

Yes, I think that's perfect.

---

View entire conversation on ReviewNB

[jessegrabowski]

I tried adding some details about each of the containers and give an example for each, let me know if it falls short of the mark.

---

View entire conversation on ReviewNB