Issue merging 2 datasets #15

Closed
opened 2020-10-26 16:55:42 +01:00 by usov_i · 11 comments
usov_i commented 2020-10-26 16:55:42 +01:00 (Migrated from gitlab.psi.ch)

Created by: ivan-usov

@JakHolzer I pushed an experimental code to the test server, in which I'm trying to merge 2 datasets:
b28fe39bbb/pyzebra/app/panel_ccl_integrate.py (L123-L125)

Running it with test data: zebra2020n000039.ccl followed by appending zebra2020n000035.dat errors with the following stack trace:

  File "/das/home/usov_i/pyzebra/pyzebra/app/panel_ccl_integrate.py", line 125, in append_upload_button_callback
    det_data = pyzebra.merge(added, added, scan_result)
  File "/das/home/usov_i/pyzebra/pyzebra/param_study_moduls.py", line 248, in merge
    if dict1["scan"][first]["monitor"] == dict2["scan"][second]["monitor"]:
KeyError: 157

Can you reproduce that? Any ideas what's wrong?

*Created by: ivan-usov* @JakHolzer I pushed an experimental code to the test server, in which I'm trying to merge 2 datasets: https://github.com/paulscherrerinstitute/pyzebra/blob/b28fe39bbb07f7426b92d4b2e5fda2f229bdfe41/pyzebra/app/panel_ccl_integrate.py#L123-L125 Running it with test data: `zebra2020n000039.ccl` followed by appending `zebra2020n000035.dat` errors with the following stack trace: ``` File "/das/home/usov_i/pyzebra/pyzebra/app/panel_ccl_integrate.py", line 125, in append_upload_button_callback det_data = pyzebra.merge(added, added, scan_result) File "/das/home/usov_i/pyzebra/pyzebra/param_study_moduls.py", line 248, in merge if dict1["scan"][first]["monitor"] == dict2["scan"][second]["monitor"]: KeyError: 157 ``` Can you reproduce that? Any ideas what's wrong?
usov_i commented 2020-10-26 17:09:07 +01:00 (Migrated from gitlab.psi.ch)

Created by: JakHolzer

Hello Ivan,
I'm away from the computer at the moment, but I think it could be caused by
not assigning the monitor value in dat file perhaps. I will check when
I get home from supermarket.

Best wishes,
Jakub

On Mon, 26 Oct 2020, 16:55 Ivan Usov, notifications@github.com wrote:

@JakHolzer https://github.com/JakHolzer I pushed an experimental code
to the test server, in which I'm trying to merge 2 datasets:

b28fe39bbb/pyzebra/app/panel_ccl_integrate.py (L123-L125)

Running it with test data: zebra2020n000039.ccl followed by appending
zebra2020n000035.dat errors with the following stack trace:

File "/das/home/usov_i/pyzebra/pyzebra/app/panel_ccl_integrate.py", line 125, in append_upload_button_callback
det_data = pyzebra.merge(added, added, scan_result)
File "/das/home/usov_i/pyzebra/pyzebra/param_study_moduls.py", line 248, in merge
if dict1["scan"][first]["monitor"] == dict2["scan"][second]["monitor"]:
KeyError: 157

Can you reproduce that? Any ideas what's wrong?


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*Created by: JakHolzer* Hello Ivan, I'm away from the computer at the moment, but I think it could be caused by not assigning the monitor value in dat file perhaps. I will check when I get home from supermarket. Best wishes, Jakub On Mon, 26 Oct 2020, 16:55 Ivan Usov, <notifications@github.com> wrote: > @JakHolzer <https://github.com/JakHolzer> I pushed an experimental code > to the test server, in which I'm trying to merge 2 datasets: > > https://github.com/paulscherrerinstitute/pyzebra/blob/b28fe39bbb07f7426b92d4b2e5fda2f229bdfe41/pyzebra/app/panel_ccl_integrate.py#L123-L125 > > Running it with test data: zebra2020n000039.ccl followed by appending > zebra2020n000035.dat errors with the following stack trace: > > File "/das/home/usov_i/pyzebra/pyzebra/app/panel_ccl_integrate.py", line 125, in append_upload_button_callback > det_data = pyzebra.merge(added, added, scan_result) > File "/das/home/usov_i/pyzebra/pyzebra/param_study_moduls.py", line 248, in merge > if dict1["scan"][first]["monitor"] == dict2["scan"][second]["monitor"]: > KeyError: 157 > > Can you reproduce that? Any ideas what's wrong? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <https://github.com/paulscherrerinstitute/pyzebra/issues/15>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AM2BBRTFZRW3ERB2ENF6CIDSMWLY7ANCNFSM4S7SHCBQ> > . >
usov_i commented 2020-10-26 19:08:25 +01:00 (Migrated from gitlab.psi.ch)

Created by: JakHolzer

Hello Ivan,
I reproduced the error. There is some problem with the scan function,
basically its happening because it found two matching scans, 3 and 157 and
157 and 3, but they are listed as two separate.
[33.0, 16.5, 138.8, -23.3] [(3, 157)]
[32.8, 16.4, 138.8, -23.0] [(157, 3)]

therefore, when the merge runs, it merges 157 into 3 and than it tries to
run again and merge 3 with 157, but 157 was deleted when it was merged with
3. I will try to fix it by tomorrow.
Jakub

po 26. 10. 2020 v 16:55 odesílatel Ivan Usov notifications@github.com
napsal:

@JakHolzer https://github.com/JakHolzer I pushed an experimental code
to the test server, in which I'm trying to merge 2 datasets:

b28fe39bbb/pyzebra/app/panel_ccl_integrate.py (L123-L125)

Running it with test data: zebra2020n000039.ccl followed by appending
zebra2020n000035.dat errors with the following stack trace:

File "/das/home/usov_i/pyzebra/pyzebra/app/panel_ccl_integrate.py", line 125, in append_upload_button_callback
det_data = pyzebra.merge(added, added, scan_result)
File "/das/home/usov_i/pyzebra/pyzebra/param_study_moduls.py", line 248, in merge
if dict1["scan"][first]["monitor"] == dict2["scan"][second]["monitor"]:
KeyError: 157

Can you reproduce that? Any ideas what's wrong?


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*Created by: JakHolzer* Hello Ivan, I reproduced the error. There is some problem with the scan function, basically its happening because it found two matching scans, 3 and 157 and 157 and 3, but they are listed as two separate. [33.0, 16.5, 138.8, -23.3] [(3, 157)] [32.8, 16.4, 138.8, -23.0] [(157, 3)] therefore, when the merge runs, it merges 157 into 3 and than it tries to run again and merge 3 with 157, but 157 was deleted when it was merged with 3. I will try to fix it by tomorrow. Jakub po 26. 10. 2020 v 16:55 odesílatel Ivan Usov <notifications@github.com> napsal: > @JakHolzer <https://github.com/JakHolzer> I pushed an experimental code > to the test server, in which I'm trying to merge 2 datasets: > > https://github.com/paulscherrerinstitute/pyzebra/blob/b28fe39bbb07f7426b92d4b2e5fda2f229bdfe41/pyzebra/app/panel_ccl_integrate.py#L123-L125 > > Running it with test data: zebra2020n000039.ccl followed by appending > zebra2020n000035.dat errors with the following stack trace: > > File "/das/home/usov_i/pyzebra/pyzebra/app/panel_ccl_integrate.py", line 125, in append_upload_button_callback > det_data = pyzebra.merge(added, added, scan_result) > File "/das/home/usov_i/pyzebra/pyzebra/param_study_moduls.py", line 248, in merge > if dict1["scan"][first]["monitor"] == dict2["scan"][second]["monitor"]: > KeyError: 157 > > Can you reproduce that? Any ideas what's wrong? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <https://github.com/paulscherrerinstitute/pyzebra/issues/15>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AM2BBRTFZRW3ERB2ENF6CIDSMWLY7ANCNFSM4S7SHCBQ> > . >
usov_i commented 2020-10-26 21:17:59 +01:00 (Migrated from gitlab.psi.ch)

Created by: JakHolzer

I was trying to find some way to fi it permanently, but could not really do
it simply. The fix I did kind of works, but it will suffer from the same
problem, in the future. It will probably have to be rewritten and I'm not
yet sure how. When we worked with hkl, i created the dictionary where the
keys are the hkl and values are the numbers of the scan and it worked well,
because the hkl was precise every time, i.e. it was always 1 0 1, not 0.98
0.001 1.01 Now this is the case and root for the problem here, it the bug
you reported, the scans with angles:
[32.97, 16.48, 138.81, -23.26]
[32.84, 16.42, 138.82, -22.97]
gets matched, which is correct, but are saved with rounded second digit.
i.e:
[33.0, 16.5, 138.8, -23.3] [(3, 157)]
[32.8, 16.4, 138.8, -23.0] [(157, 3)]
so it thinks that there are two scans. the correct way should be:
[33.0, 16.0, 139.0, -23.0] [(3, 157), (157, 3)], which it does now, but it
will fail happily when one of the angles in first scan will be 1.4 and in
second 1.6. I will try to come up with a better solution, perhaps filter
the reverse duplicates from the beginning. Any hints welcomed 😓

I will try to come up with something quickly.
Best,
Jakub

po 26. 10. 2020 v 19:08 odesílatel Jakub Holzer holzer.jakub@gmail.com
napsal:

Hello Ivan,
I reproduced the error. There is some problem with the scan function,
basically its happening because it found two matching scans, 3 and 157 and
157 and 3, but they are listed as two separate.
[33.0, 16.5, 138.8, -23.3] [(3, 157)]
[32.8, 16.4, 138.8, -23.0] [(157, 3)]

therefore, when the merge runs, it merges 157 into 3 and than it tries to
run again and merge 3 with 157, but 157 was deleted when it was merged with
3. I will try to fix it by tomorrow.
Jakub

po 26. 10. 2020 v 16:55 odesílatel Ivan Usov notifications@github.com
napsal:

@JakHolzer https://github.com/JakHolzer I pushed an experimental code
to the test server, in which I'm trying to merge 2 datasets:

b28fe39bbb/pyzebra/app/panel_ccl_integrate.py (L123-L125)

Running it with test data: zebra2020n000039.ccl followed by appending
zebra2020n000035.dat errors with the following stack trace:

File "/das/home/usov_i/pyzebra/pyzebra/app/panel_ccl_integrate.py", line 125, in append_upload_button_callback
det_data = pyzebra.merge(added, added, scan_result)
File "/das/home/usov_i/pyzebra/pyzebra/param_study_moduls.py", line 248, in merge
if dict1["scan"][first]["monitor"] == dict2["scan"][second]["monitor"]:
KeyError: 157

Can you reproduce that? Any ideas what's wrong?


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Reply to this email directly, view it on GitHub
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*Created by: JakHolzer* I was trying to find some way to fi it permanently, but could not really do it simply. The fix I did kind of works, but it will suffer from the same problem, in the future. It will probably have to be rewritten and I'm not yet sure how. When we worked with hkl, i created the dictionary where the keys are the hkl and values are the numbers of the scan and it worked well, because the hkl was precise every time, i.e. it was always 1 0 1, not 0.98 0.001 1.01 Now this is the case and root for the problem here, it the bug you reported, the scans with angles: [32.97, 16.48, 138.81, -23.26] [32.84, 16.42, 138.82, -22.97] gets matched, which is correct, but are saved with rounded second digit. i.e: [33.0, 16.5, 138.8, -23.3] [(3, 157)] [32.8, 16.4, 138.8, -23.0] [(157, 3)] so it thinks that there are two scans. the correct way should be: [33.0, 16.0, 139.0, -23.0] [(3, 157), (157, 3)], which it does now, but it will fail happily when one of the angles in first scan will be 1.4 and in second 1.6. I will try to come up with a better solution, perhaps filter the reverse duplicates from the beginning. Any hints welcomed 😓 I will try to come up with something quickly. Best, Jakub po 26. 10. 2020 v 19:08 odesílatel Jakub Holzer <holzer.jakub@gmail.com> napsal: > Hello Ivan, > I reproduced the error. There is some problem with the scan function, > basically its happening because it found two matching scans, 3 and 157 and > 157 and 3, but they are listed as two separate. > [33.0, 16.5, 138.8, -23.3] [(3, 157)] > [32.8, 16.4, 138.8, -23.0] [(157, 3)] > > therefore, when the merge runs, it merges 157 into 3 and than it tries to > run again and merge 3 with 157, but 157 was deleted when it was merged with > 3. I will try to fix it by tomorrow. > Jakub > > po 26. 10. 2020 v 16:55 odesílatel Ivan Usov <notifications@github.com> > napsal: > >> @JakHolzer <https://github.com/JakHolzer> I pushed an experimental code >> to the test server, in which I'm trying to merge 2 datasets: >> >> https://github.com/paulscherrerinstitute/pyzebra/blob/b28fe39bbb07f7426b92d4b2e5fda2f229bdfe41/pyzebra/app/panel_ccl_integrate.py#L123-L125 >> >> Running it with test data: zebra2020n000039.ccl followed by appending >> zebra2020n000035.dat errors with the following stack trace: >> >> File "/das/home/usov_i/pyzebra/pyzebra/app/panel_ccl_integrate.py", line 125, in append_upload_button_callback >> det_data = pyzebra.merge(added, added, scan_result) >> File "/das/home/usov_i/pyzebra/pyzebra/param_study_moduls.py", line 248, in merge >> if dict1["scan"][first]["monitor"] == dict2["scan"][second]["monitor"]: >> KeyError: 157 >> >> Can you reproduce that? Any ideas what's wrong? >> >> — >> You are receiving this because you were mentioned. >> Reply to this email directly, view it on GitHub >> <https://github.com/paulscherrerinstitute/pyzebra/issues/15>, or >> unsubscribe >> <https://github.com/notifications/unsubscribe-auth/AM2BBRTFZRW3ERB2ENF6CIDSMWLY7ANCNFSM4S7SHCBQ> >> . >> >
usov_i commented 2020-10-27 10:34:04 +01:00 (Migrated from gitlab.psi.ch)

Created by: ivan-usov

I didn't thoroughly check the code in param_study_moduls.py, but to my understanding, merging should happen in-place like in the following pseudo code:

def merge(d1, d2):
    if d1_meta incompatible with d2_meta:
        raise ValueError("Incompatible metadata")

    for scan in d2_scans:
        if scan in d1_scans:  # based on angles or hkl
            d1_scans.replace_or_sum(scan)
        else:
            d1_scans.append_as_new(scan)

Maybe d1_meta needs some updates too, I don't know. But I also don't understand what you're trying to achieve by splitting this single operation into all these functions.

*Created by: ivan-usov* I didn't thoroughly check the code in `param_study_moduls.py`, but to my understanding, merging should happen in-place like in the following pseudo code: ```python def merge(d1, d2): if d1_meta incompatible with d2_meta: raise ValueError("Incompatible metadata") for scan in d2_scans: if scan in d1_scans: # based on angles or hkl d1_scans.replace_or_sum(scan) else: d1_scans.append_as_new(scan) ``` Maybe d1_meta needs some updates too, I don't know. But I also don't understand what you're trying to achieve by splitting this single operation into all these functions.
usov_i commented 2020-10-27 10:42:47 +01:00 (Migrated from gitlab.psi.ch)

Created by: JakHolzer

Well, the idea at the beginning was to have some sort of output for the
user to check what is in the ccls and decide. The list of matching scans
was also meant be used for other operations, such as point by point
subtraction, but it obviously doesent work. I will write something with
your idea. Thanks!

út 27. 10. 2020 v 10:34 odesílatel Ivan Usov notifications@github.com
napsal:

I didn't thoroughly check the code in param_study_moduls.py, but to my
understanding, merging should happen in-place like in the following pseudo
code:

def merge(d1, d2):
if d1_meta incompatible with d2_meta:
raise ValueError("Incompatible metadata")

for scan in d2_scans:
    if scan in d1_scans:  # based on angles or hkl
        d1_scans.replace_or_sum(scan)
    else:
        d1_scans.append_as_new(scan)

Maybe d1_meta needs some updates too, I don't know. But I also don't
understand what you're trying to achieve by splitting this single operation
into all these functions.


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*Created by: JakHolzer* Well, the idea at the beginning was to have some sort of output for the user to check what is in the ccls and decide. The list of matching scans was also meant be used for other operations, such as point by point subtraction, but it obviously doesent work. I will write something with your idea. Thanks! út 27. 10. 2020 v 10:34 odesílatel Ivan Usov <notifications@github.com> napsal: > I didn't thoroughly check the code in param_study_moduls.py, but to my > understanding, merging should happen in-place like in the following pseudo > code: > > def merge(d1, d2): > if d1_meta incompatible with d2_meta: > raise ValueError("Incompatible metadata") > > for scan in d2_scans: > if scan in d1_scans: # based on angles or hkl > d1_scans.replace_or_sum(scan) > else: > d1_scans.append_as_new(scan) > > Maybe d1_meta needs some updates too, I don't know. But I also don't > understand what you're trying to achieve by splitting this single operation > into all these functions. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <https://github.com/paulscherrerinstitute/pyzebra/issues/15#issuecomment-717111204>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AM2BBRRQBU3C7JPCNG4TNX3SM2HZ5ANCNFSM4S7SHCBQ> > . >
usov_i commented 2020-10-27 11:07:15 +01:00 (Migrated from gitlab.psi.ch)

Created by: ivan-usov

Let's keep it as simple as possible. I don't expect that, practically, users will need to look at what they have in both files and then decide to merge or not.

Here we handle just the first step of merging one datasets (.ccl) with an additional scan (.dat) or another dataset (.ccl). Point by point subtraction, as far as I understood, happens between datasets after all fitting etc. So, let's not consider it yet, because it will be a different operation.

*Created by: ivan-usov* Let's keep it as simple as possible. I don't expect that, practically, users will need to look at what they have in both files and then decide to merge or not. Here we handle just the first step of merging one datasets (.ccl) with an additional scan (.dat) or another dataset (.ccl). Point by point subtraction, as far as I understood, happens between datasets after all fitting etc. So, let's not consider it yet, because it will be a different operation.
usov_i commented 2020-10-27 11:17:53 +01:00 (Migrated from gitlab.psi.ch)

Created by: JakHolzer

Alright, I would go now with the yesterdays fix and I will supply new
function soon.

út 27. 10. 2020 v 11:07 odesílatel Ivan Usov notifications@github.com
napsal:

Let's keep it as simple as possible. I don't expect that, practically,
users will need to look at what they have in both files and then decide to
merge or not.

Here we handle just the first step of merging one datasets (.ccl) with an
additional scan (.dat) or another dataset (.ccl). Point by point
subtraction, as far as I understood, happens between datasets after all
fitting etc. So, let's not consider it yet, because it will be a different
operation.


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*Created by: JakHolzer* Alright, I would go now with the yesterdays fix and I will supply new function soon. út 27. 10. 2020 v 11:07 odesílatel Ivan Usov <notifications@github.com> napsal: > Let's keep it as simple as possible. I don't expect that, practically, > users will need to look at what they have in both files and then decide to > merge or not. > > Here we handle just the first step of merging one datasets (.ccl) with an > additional scan (.dat) or another dataset (.ccl). Point by point > subtraction, as far as I understood, happens between datasets after all > fitting etc. So, let's not consider it yet, because it will be a different > operation. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <https://github.com/paulscherrerinstitute/pyzebra/issues/15#issuecomment-717131042>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AM2BBRSOW7SJO2BHYNJFL43SM2LWFANCNFSM4S7SHCBQ> > . >
usov_i commented 2020-10-28 15:33:09 +01:00 (Migrated from gitlab.psi.ch)

Created by: JakHolzer

Hello Ivan,
I apologise for the delay. I was trying to rewrite the function in the
manner you suggested, but still running into problems such as runtime
errors cause by dictionary change or keyerrors caused by deleted scans.
This always leads me to similar solutions where the process is split into
two function, where one scans and gives output to the second, that merges.
Generally, it is necessary to scan the ccl files, because sometimes there
can be repeated scans even before merging with other datasets. I will keep
trying, but progress has not been great so far.

Best,
Jakub

út 27. 10. 2020 v 11:18 odesílatel Jakub Holzer holzer.jakub@gmail.com
napsal:

Alright, I would go now with the yesterdays fix and I will supply new
function soon.

út 27. 10. 2020 v 11:07 odesílatel Ivan Usov notifications@github.com
napsal:

Let's keep it as simple as possible. I don't expect that, practically,
users will need to look at what they have in both files and then decide to
merge or not.

Here we handle just the first step of merging one datasets (.ccl) with an
additional scan (.dat) or another dataset (.ccl). Point by point
subtraction, as far as I understood, happens between datasets after all
fitting etc. So, let's not consider it yet, because it will be a different
operation.


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*Created by: JakHolzer* Hello Ivan, I apologise for the delay. I was trying to rewrite the function in the manner you suggested, but still running into problems such as runtime errors cause by dictionary change or keyerrors caused by deleted scans. This always leads me to similar solutions where the process is split into two function, where one scans and gives output to the second, that merges. Generally, it is necessary to scan the ccl files, because sometimes there can be repeated scans even before merging with other datasets. I will keep trying, but progress has not been great so far. Best, Jakub út 27. 10. 2020 v 11:18 odesílatel Jakub Holzer <holzer.jakub@gmail.com> napsal: > Alright, I would go now with the yesterdays fix and I will supply new > function soon. > > út 27. 10. 2020 v 11:07 odesílatel Ivan Usov <notifications@github.com> > napsal: > >> Let's keep it as simple as possible. I don't expect that, practically, >> users will need to look at what they have in both files and then decide to >> merge or not. >> >> Here we handle just the first step of merging one datasets (.ccl) with an >> additional scan (.dat) or another dataset (.ccl). Point by point >> subtraction, as far as I understood, happens between datasets after all >> fitting etc. So, let's not consider it yet, because it will be a different >> operation. >> >> — >> You are receiving this because you were mentioned. >> Reply to this email directly, view it on GitHub >> <https://github.com/paulscherrerinstitute/pyzebra/issues/15#issuecomment-717131042>, >> or unsubscribe >> <https://github.com/notifications/unsubscribe-auth/AM2BBRSOW7SJO2BHYNJFL43SM2LWFANCNFSM4S7SHCBQ> >> . >> >
usov_i commented 2020-10-30 14:39:21 +01:00 (Migrated from gitlab.psi.ch)

Created by: ivan-usov

@JakHolzer , there is now two files with operations for dictionary scanning and merging. I assume that the old file ccl_dict_operation.py is not supported anymore and can be removed?

*Created by: ivan-usov* @JakHolzer , there is now two files with operations for dictionary scanning and merging. I assume that the old file `ccl_dict_operation.py` is not supported anymore and can be removed?
usov_i commented 2020-10-30 14:41:24 +01:00 (Migrated from gitlab.psi.ch)

Created by: JakHolzer

Yes, there are some extra functions there zvut they rely on the scan_dict
function, which we are not be using anymore, once we have a suitable
function.

On Fri, 30 Oct 2020, 14:39 Ivan Usov, notifications@github.com wrote:

@JakHolzer https://github.com/JakHolzer , there is now two files with
operations for dictionary scanning and merging. I assume that the old file
ccl_dict_operation.py is not supported anymore and can be removed?


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*Created by: JakHolzer* Yes, there are some extra functions there zvut they rely on the scan_dict function, which we are not be using anymore, once we have a suitable function. On Fri, 30 Oct 2020, 14:39 Ivan Usov, <notifications@github.com> wrote: > @JakHolzer <https://github.com/JakHolzer> , there is now two files with > operations for dictionary scanning and merging. I assume that the old file > ccl_dict_operation.py is not supported anymore and can be removed? > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <https://github.com/paulscherrerinstitute/pyzebra/issues/15#issuecomment-719557910>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AM2BBRQO5JPUBNZQVTD3EVTSNK6ZPANCNFSM4S7SHCBQ> > . >
usov_i commented 2021-02-12 17:00:22 +01:00 (Migrated from gitlab.psi.ch)

Created by: ivan-usov

The merging procedure was refactored, so the issue is not actual anymore

*Created by: ivan-usov* The merging procedure was refactored, so the issue is not actual anymore
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Reference: zebra/pyzebra#15
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