Add Theory of Change Framework preprint

[sakshimohan]

Added preprint to publication list.

[sakshimohan]

@matt-graham @tbhallett I have added this publication to the Zotero library. But I haven't been succesful with step 3 of the process.

When I run in the tlo environment
tox -e update-publications
I get the following error -
ROOT: HandledError| provided environments not found in configuration file: update-publications

[matt-graham]

Hi @sakshimohan. Are you running the tox -e update-publications command from the root the TLOmodel repository and with the most recent version of master checked out? The error you got suggests tox is not able to find the update-publications environment defined in the tox.ini file - this was added in #1507 so should be available. You can also try running

python /home/matt/projects/TLOmodel/docs/tlo_publications.py --update-from-zotero

to directly run the script, but you will also need to run pip install pybtex requests first in this case to install the additional dependencies the script needs (tox deals with this automatically).

[sakshimohan]

Hi @sakshimohan. Are you running the tox -e update-publications command from the root the TLOmodel repository and with the most recent version of master checked out? The error you got suggests tox is not able to find the update-publications environment defined in the tox.ini file - this was added in #1507 so should be available. You can also try running

python /home/matt/projects/TLOmodel/docs/tlo_publications.py --update-from-zotero

to directly run the script, but you will also need to run pip install pybtex requests first in this case to install the additional dependencies the script needs (tox deals with this automatically).

Many thanks, @matt-graham . That problem is resolved. I get the following different error now -
File "/Users/sm2511/PycharmProjects/TLOmodel/docs/tlo_publications.py", line 103 toplevel[ ^^^^^^^^^ SyntaxError: invalid syntax. Perhaps you forgot a comma?

[matt-graham]

Many thanks, @matt-graham . That problem is resolved. I get the following different error now - File "/Users/sm2511/PycharmProjects/TLOmodel/docs/tlo_publications.py", line 103 toplevel[ ^^^^^^^^^ SyntaxError: invalid syntax. Perhaps you forgot a comma?

Oh that's an interesting one! That's suggesting there is a syntax error in

TLOmodel/docs/tlo_publications.py

Lines 103 to 108 in 49acef5

	toplevel[
	*(
	tag("tr")[toplevel[tag("td")[tag("em")[key]], tag("td")[value]]]
	for key, value in details.items()
	)
	]

which confusingly does not create any syntax errors when running for me 😕

Can I check what Python version you have and what the version pybtex that got installed was (should be able to check from Python packages tab / dialog in PyCharm or by running pip list pybtex in a terminal)?

[sakshimohan]

Many thanks, @matt-graham . That problem is resolved. I get the following different error now - File "/Users/sm2511/PycharmProjects/TLOmodel/docs/tlo_publications.py", line 103 toplevel[ ^^^^^^^^^ SyntaxError: invalid syntax. Perhaps you forgot a comma?

Oh that's an interesting one! That's suggesting there is a syntax error in

TLOmodel/docs/tlo_publications.py

Lines 103 to 108 in 49acef5

	toplevel[
	*(
	tag("tr")[toplevel[tag("td")[tag("em")[key]], tag("td")[value]]]
	for key, value in details.items()
	)
	]

which confusingly does not create any syntax errors when running for me 😕

Can I check what Python version you have and what the version pybtex that got installed was (should be able to check from Python packages tab / dialog in PyCharm or by running pip list pybtex in a terminal)?

I've got -
pybtex 0.24.0
Python version 3.10.13

[matt-graham]

Ah this could be an issue with the use of *(...) with a generator expression in the indexing operation as this seems to only work on Python 3.11+

As a more minimal example

import numpy as np
array = np.arange(12).reshape(3, 4)
array[*(i for i in range(1, 3))]

runs fine for me on Python 3.11+ but gives a syntax error in Python 3.10.

[sakshimohan]

Ah this could be an issue with the use of *(...) with a generator expression in the indexing operation as this seems to only work on Python 3.11+

As a more minimal example

import numpy as np
array = np.arange(12).reshape(3, 4)
array[*(i for i in range(1, 3))]

runs fine for me on Python 3.11+ but gives a syntax error in Python 3.10.

Got I will update to Python 11 in this case. Are you OK to merge this PR into master anyway?
I'm reluctant to update today because I have a deliverable due this evening and I'm afraid my analysis code might run into unexpected issues with the update which I will not have the time to address today.

[matt-graham]

I've got - pybtex 0.24.0 Python version 3.10.13

Probably worth updating to Python 3.11 as that is what we are currently recommending and testing against. For a quickfix for now to get this running in your Python 3.10 you can just change

 toplevel[ 
     *( 
         tag("tr")[toplevel[tag("td")[tag("em")[key]], tag("td")[value]]] 
         for key, value in details.items() 
     ) 
 ] 

to

 toplevel[ 
     tuple( 
         tag("tr")[toplevel[tag("td")[tag("em")[key]], tag("td")[value]]] 
         for key, value in details.items() 
     ) 
 ] 

that is swap * for tuple in docs/tlo_publications.py.

To update your environment to Python 3.11 the easiest way is to delete your current Conda environment

conda remove -n tlo --all

and the follow the installation instructions to create a new Python 3.11 environment with the dependencies.

[matt-graham]

Got I will update to Python 11 in this case. Are you OK to merge this PR into master anyway? I'm reluctant to update today because I have a deliverable due this evening and I'm afraid my analysis code might run into unexpected issues with the update which I will not have the time to address today.

Sorry missed this while writing previous message! Yes that's fine, once the checks / documentation workflows finish running I'll merge this assuming they pass!