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Migrate open source docs (attempt #2) #118

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merged 142 commits into from
Oct 9, 2023
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Recreates #91, but without squash merging.

derivation and others added 30 commits May 1, 2019 20:44
* fixes Qiskit/qiskit-metapackage#113

* added link to install instructions

fixed some styles

* Review changes

- Add Q&A Format
* Updated Getting Started

* Removed trailing whitespaces and long lines

* Removed typo

* eliminated build  warnings

* eliminated build  warnings in getting started

* edit getting_started

* edit executing quantum programs

* Update executing_quantum_programs.rst

line length

* fix code block formatting

* fix circuit drawings

* fix plain text code block syntax

* update IBM Q Experience link
* Update install docs

* Load.account() updates

* Update get.backend

* Add update link

* Fix link

* Fix typos

* Address review comments

* Fix line length
* Standardized hyperlinks and underscores

* Fixed lint errors
…other_optims

Add other optimization notebooks and fixes
* Set up CI with Azure Pipelines

This commit adds the CI configuration for running sphinx builds in CI. [skip ci]

* Add missing dep and start caching pip

* Install pandoc and graphviz

* Add cvxpy install for aer noise transformations

* Move aqua tutorials that depend on CPLEX to legacy_tutorials

There are 2 aqua tutorials that do not work unless CPLEX is installed.
CPLEX is too involved and difficult to install in CI. It is also
proprietary software which prohibits installing it in CI (since a CI
system can't agree to the license terms). Honestly, I'm not entirely
sure why aqua has modules in it that depend solely on having proprietary
software installed, it feels like there should be an open alternative or
if there is one already the tutorial should leverage that. To make the
docs buildable this commit moves these problematic tutorials to the
legacy directory so they're not built/run by default.

* Workaround terra mpl drawer bug

There is a bug in the mpl drawer in 0.19.0 (and 0.19.1) release where a
custom instruction does not draw without a label parameter set. This
will need to be fixed in terra, but in the meantime this worksaround the
bug by manually setting a label.

* Add texlive to installed packages

* Install correct texlive metapackage with qcircuit

* Correct package name again

* Add another missing binary dep

* Update qcircuit version as packaged version is too old

* Try using tlmgr instead of manually downloading qcircuit

* Try using more from tlmgr instead of apt

* Fix typo

* Use bash directly

* Adjust texlive update script usage

* Give up on tlmgr and try to manual install qcircuit again

* Fix typo

* revert aqua tutorial move and remove latex install

* Remove section of aqua notebook 2 that requires cplex

* Remove another notebook with cplex
…circuits_1

fix spacing around equations in circuits_1
…transpiler_notebook

Update 4_transpiler_passes_and_passmanager.ipynb
I found it confusing when reading initially, and hence wanted to reiterate that the qubit representing
the MSB is left-most, indexed with 0.
Minor improvements to Getting Started tutorials.
SooluThomas and others added 23 commits June 15, 2023 17:08
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### Summary

Fixed typo.

### Details and comments
intial -> initial

Co-authored-by: mergify[bot] <37929162+mergify[bot]@users.noreply.github.com>
DeprecationWarning: The module 'qiskit.test.mock' is deprecated since
Qiskit Terra 0.21.0, and will be removed 3 months or more later.
Instead, you should import the desired object directly
'qiskit.providers.fake_provider'.
#from qiskit.test.mock import FakeVigo --> 
from qiskit.providers.fake_provider import FakeVigo
(https://qiskit.org/documentation/apidoc/providers_fake_provider.html)

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### Summary
DeprecationWarning: The module 'qiskit.test.mock'


### Details and comments
DeprecationWarning: The module 'qiskit.test.mock' is deprecated since
Qiskit Terra 0.21.0, and will be removed 3 months or more later.
Instead, you should import the desired object directly
'qiskit.providers.fake_provider'.
#from qiskit.test.mock import FakeVigo -->
from qiskit.providers.fake_provider import FakeVigo
(https://qiskit.org/documentation/apidoc/providers_fake_provider.html)

---------

Co-authored-by: Junye Huang <h.jun.ye@gmail.com>
Co-authored-by: Eric Arellano <14852634+Eric-Arellano@users.noreply.github.com>
…it-tutorials#1165)

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### Summary
Fixing layer description in "Implementing a BasicMapper Pass"


### Details and comments
Original sentence stated "each layer is a group of operations that does
not act on independent qubits, so in theory all operations in a layer
can be done independently", which is incorrect. Every layer is a group
of operations specifically acting on separate qubits each. The new
sentence clarifies that with "each layer is a group of operations acting
on independent qubits..."

Co-authored-by: Eric Arellano <14852634+Eric-Arellano@users.noreply.github.com>
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### Summary
I have coded a script which (when directory is specified) checks for the
broken links in the Jupyter notebooks and tells its exact place and the
error it shows.
```
import os
import nbformat as nbf
import re
import requests
# Code to populate file_list with relevant .ipynb files
file_list = []

for root, dirs, files in os.walk("qiskit-tutorials/tutorials/"):
    for file in files:
        if file.endswith(".ipynb"):
            file_list.append(os.path.join(root, file))  # Including the relative path of the file

INLINE_LINK_RE = re.compile(r'\[([^\]]+)\]\(([^)]+)\)')
for file_path in file_list:
    try:
        with open(file_path) as file:
            nb = nbf.read(file, 4)
    except OSError as e:
        print(f"Error occurred while reading file: {file_path}")
        print("Error message:", str(e))
        print()
        continue

    for cell in nb["cells"]:
        if cell["cell_type"] != "markdown":
            continue
        links = list(INLINE_LINK_RE.findall(cell["source"]))
        for link in links:
            if not link:
                continue
            link_text, link_url = link
            if link_url.lower().endswith(('.png', '.jpg', '.jpeg', '.gif')):
                continue  # Skip image links
            try:
                response = requests.get(link_url)
                if response.status_code != 200:
                    print(f"Broken link found in file: {file_path}")
                    print(f"Link: {link_text}")
                    print(f"URL: {link_url}")
                    print("HTTP status code:", response.status_code)
                    print()
            except requests.RequestException as e:
                print(f"Error occurred while checking link in file: {file_path}")
                print(f"Link: {link_text}")
                print(f"URL: {link_url}")
                print("Error message:", str(e))
                print()

```

### Details and comments

This code is part of QAMP Project [Issues in Qiskit Tutorials
Qiskit/qiskit-tutorials#37](qiskit-advocate/qamp-spring-23#37)
which can read many files at once and can find broken links with their
exact position and error code it is showing.

I ran this above code throughout the repo and checked each and every
Jupyter notebook files, based on the output I have fixed many links.
This PR is just the Last PR of the of project, which fixes the remaining
broken links. All the other broken links are already fixed in the past
PRs which are made throughout this project. Qiskit/qiskit-tutorials#1445 Qiskit/qiskit-tutorials#1446 Qiskit/qiskit-tutorials#1467 Qiskit/qiskit-tutorials#1483
Qiskit/qiskit-tutorials#1484.
This project also fixes Qiskit/qiskit-tutorials#1402
)

### Summary
The function plot_histogram() in the text should be `plot_histogram()`


### Details and comments

---------

Co-authored-by: Eric Arellano <ericarellano@me.com>
This cross-repository merge unifies the documentation, benchmarks and
code of conduct from the metapackage into Qiskit/Terra's build.

There are very non-trivial merge conflicts that have been resolved by
this commit.  The summary is:

- `CODE_OF_CONDUCT.md`: taken directly from the metapackage's version.
- `docs/conf.py`: strongly unified, albeit without the translations
  components that are added in a separate commit.
- `docs/index.rst`: taken almost verbatim from the metapackage.  All the
  API documentation RST files on Terra are moved to `docs/apidoc`
  (without the trailing 's') to match the metapackage expectation, so
  the URLs of built documentation will not change.
- `docs/release_notes.rst`: The metapackage's version is renamed to
  `docs/legacy_release_notes.rst`, given a small introductory header,
  and made an orphan linked only from a _new_ `docs/release_notes.rst`
  that uses `reno`.
- `docs/tutorials.rst`: Mostly these were the same already.  Updated to
  include Qiskit/Terra's correction that it's not an orphan, and contain
  the metapackage's extra intro tutorial.
- `docs/apidoc/terra.rst`: renamed to `docs/apidoc/index.rst` and retitled
  to be correctly just "API Documentation".
- `requirements-dev.txt`: the version of the Sphinx theme is bumped to 1.14
  to match the metapackage expectation.
…10611)

### Summary

This cross-repository merge unifies the documentation, benchmarks and
code of conduct from the metapackage into Qiskit/Terra's build.

There are very non-trivial merge conflicts that have been resolved by
this commit. The summary is:

- `CODE_OF_CONDUCT.md`: taken directly from the metapackage's version.
- `docs/conf.py`: strongly unified, albeit without the translations
components that are added in a separate commit.
- `docs/index.rst`: taken almost verbatim from the metapackage. All the
API documentation RST files on Terra are moved to `docs/apidoc` (without
the trailing 's') to match the metapackage expectation, so the URLs of
built documentation will not change.
- `docs/release_notes.rst`: The metapackage's version is renamed to
`docs/legacy_release_notes.rst`, given a small introductory header, and
made an orphan linked only from a _new_ `docs/release_notes.rst` that
uses `reno`.
- `docs/tutorials.rst`: Mostly these were the same already. Updated to
include Qiskit/Terra's correction that it's not an orphan, and contain
the metapackage's extra intro tutorial.
- `docs/apidoc/terra.rst`: renamed to `docs/apidoc/index.rst` and
retitled to be correctly just "API Documentation".
- `requirements-dev.txt`: the version of the Sphinx theme is bumped to
1.14 to match the metapackage expectation.

Following merge commit 22a406c, there is a commit 66a5d9fe0 that fixes
the ASV build for use in Terra, which is the rollup of the post-merge
commits of Qiskit/qiskit#10546, which this PR supersedes.


### Details and comments

This should probably be merged ASAP before `main` moves on.

Resolutions on the metapackage:
- Fix Qiskit/qiskit-metapackage#1723
- Fix Qiskit/qiskit-metapackage#1722
- Fix Qiskit/qiskit-metapackage#1746

After this has merged, Qiskit/qiskit#10610 should merge which will close the
remaining migration-related issues from the metapackage.

The metapackage was prepared for the migration using
[`git-filter-repo`](https://github.com/newren/git-filter-repo), with the
scripts and configuration files contained within
[metapackage_migration.zip](https://github.com/Qiskit/qiskit-terra/files/12324298/metapackage_migration.zip).
If you extract that zip, you need to activate a Python 3.11 `venv` then
run `metapackage_rewrite.bash` which will prepare the repo in the exact
state I merged to create this PR.

*edit*: In retrospect writing this, you might need to modify my script
so that it pulls only starting from commit
Qiskit/qiskit-metapackage@f131daf, which was the tip of `master` at the
time I ran this.

I tested the docs build locally and it looks as correct as I can tell.
There's still big cards pointing to experiments, dynamics etc on the
landing page, but I figured that enough's enough, and we can just fix
those last two things in Terra. This PR does not include
Qiskit/qiskit-metapackage#1791, which should be now cherry-picked onto
Terra.
…ity matrix' (Qiskit/qiskit-tutorials#1196)

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### Summary
As described in issue Qiskit/qiskit-tutorials#1189, "state matrix" has been replaced by
"density matrix" in `plot_state_city` and
`plot_state_hinton` fotutorials/circuits/2_plotting_data_in_qiskit.html.
Additionally I have also changed it at other plot functions.


### Details and comments
"State matrix" has a different physical meaning and doesn't go with the
definition given in the documentation. Hence "density matrix" seems like
a better option to use instead of "state matrix".

Co-authored-by: Eric Arellano <14852634+Eric-Arellano@users.noreply.github.com>
…ials#1231)

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### Summary
Fix a typo, in cell with description "# Compose YX in front of the
previous operator". The code compose XZ in front of the previous
operator, while it should be YX.


### Details and comments
`op.compose(XZ, qargs=[0, 2], front=True)` is changed with
`op.compose(YX, qargs=[0, 2], front=True)`, and add the correct output.

---------

Co-authored-by: Eric Arellano <14852634+Eric-Arellano@users.noreply.github.com>
…t-tutorials#1494)

Built on top of Qiskit/qiskit-tutorials#1239.

---------

Co-authored-by: Bochen "Daniel" Tan <33230390+tbcdebug@users.noreply.github.com>
* update doc

* hooray for spellchecker

* Apply suggestions from code review

Co-authored-by: Rebecca Dimock <66339736+beckykd@users.noreply.github.com>

* Update docs/faqs/max_execution_time.rst

Co-authored-by: Rebecca Dimock <66339736+beckykd@users.noreply.github.com>

---------

Co-authored-by: Rebecca Dimock <66339736+beckykd@users.noreply.github.com>
https://github.com/Qiskit/qiskit-tutorials has been archived because the
docs are now built in this repository and we want to simplify our docs
infrastructure.

This PR merges the qiskit-tutorials repository here for the relevant
tutorials, preserving its Git history. It uses `git-filter-repo` to
tweak the Git history of `qiskit-tutorials` to be consumable in this
repository, such as changing of `tutorials/` to be `docs/tutorials`. It
also prunes irrelevant commits since we only copy over the tutorials
that are currently in use and we ignore files like README.md that aren't
copied over.

See
[tutorials_migration.zip](https://github.com/Qiskit/qiskit/files/12442282/tutorials_migration.zip)
for how the migration was generated; credit to @jakelishman for the
original script used in Qiskit/qiskit#10611.
Then, I used `git merge --allow-unrelated-histories
qiskit-tutorials/master`, with the remote `qiskit-tutorials` pointed at
the prepared local repository.

The merge was clean. This PR adds two commits on tip:

* Removes the `prepare_tutorials.bash` script and placeholder tutorials
that were used to download the tutorials from `qiskit-tutorials`
dynamically. No need now that they live in the same repository.
* Updates the tutorials with the most recently executed versions from
CI.
* Initial edits

* edit

* Update docs/faqs/max_execution_time.rst

* Update docs/faqs/max_execution_time.rst

* Update docs/faqs/max_execution_time.rst

* Update docs/faqs/max_execution_time.rst

* Update docs/faqs/max_execution_time.rst

* Update docs/faqs/max_execution_time.rst

Co-authored-by: Jessie Yu <jessieyu@us.ibm.com>

* Jessie comments

* Update docs/faqs/max_execution_time.rst

Co-authored-by: Jessie Yu <jessieyu@us.ibm.com>

* Update docs/faqs/max_execution_time.rst

Co-authored-by: Jessie Yu <jessieyu@us.ibm.com>

* Update docs/sessions.rst

* Update docs/faqs/max_execution_time.rst

---------

Co-authored-by: Jessie Yu <jessieyu@us.ibm.com>
* Don't use QPU complex

* don't use the word 'limit'

* Update docs/faqs/max_execution_time.rst

* Update qiskit_ibm_runtime/options/options.py

* Update qiskit_ibm_runtime/runtime_job.py

* Update releasenotes/notes/0.11/job-cost-estimation-d0ba83dbc95c3f67.yaml

* Clarify usage

* reclarify reset time

* rogue comma

* fix whitespace & formatting

* job -> system execution time

---------

Co-authored-by: Kevin Tian <kevin.tian@ibm.com>
* Changes for Qiskit/qiskit-ibm-runtime#1806

* Update docs/faqs/max_execution_time.rst

Co-authored-by: Jessie Yu <jessieyu@us.ibm.com>

---------

Co-authored-by: Kevin Tian <kt474@cornell.edu>
Co-authored-by: Jessie Yu <jessieyu@us.ibm.com>
Co-authored-by: Kevin Tian <kevin.tian@ibm.com>
* big moves, import still works

* most tests pass (some I cannot seem to run locally)

* fix tests -- how to remove DiagonalGate?

* typehints and docs

* more type hints

* Deprecate SQU

* deprecate Snapshot

* Fix missing future annotations import

* minimize deprecation effort

* Change to pending deprecation, no exact-location import supported

* fix MCG<->MGC typo and snapshot deprecation

* fix pylint, try fixing docs

* remove gates from extensions toctree

* Add reno, fully deprecate SQU and Snapshot

* Apply Sasha's review comments

- fix usage of .squ and .snapshot w/o import
- fix docstring usage of extensions
- fix tests

* capture snapshot deprecation warning

* review comments

- capture warning of SQU
- update reno to explicitly mention pending deprecation, add DiagonalGate and ExtensionError

* missed `diagonal` method

---------

Co-authored-by: Alexander Ivrii <alexi@il.ibm.com>
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Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you all sign our Contributor License Agreement before we can accept your contribution.
19 out of 24 committers have signed the CLA.

✅ mtreinish
✅ NG-Glen
✅ SooluThomas
✅ EmilMagni
✅ ElePT
✅ frankharkins
✅ beckykd
✅ jyu00
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✅ WhiteSymmetry
✅ 1ucian0
✅ wshanks
✅ Cryoris
✅ rht
✅ shil-m
✅ jakelishman
✅ elberttl
✅ Eric-Arellano
✅ divshacker
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❌ 3yakuya
❌ soon-teh
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@Eric-Arellano Eric-Arellano merged commit b3a61c3 into main Oct 9, 2023
3 of 4 checks passed
@Eric-Arellano Eric-Arellano deleted the migrate-open-source-rnd2 branch October 9, 2023 13:53
Eric-Arellano added a commit that referenced this pull request Oct 9, 2023
For some reason, this wasn't brought in via
#118. This uses `git
cherry-pick` to bring in the relevant commit.

Co-authored-by: Guillermo-Mijares-Vilarino <106545082+Guillermo-Mijares-Vilarino@users.noreply.github.com>
Co-authored-by: Steve Wood <40241007+woodsp-ibm@users.noreply.github.com>
Co-authored-by: Junye Huang <h.jun.ye@gmail.com>
Co-authored-by: Elena Peña Tapia <57907331+ElePT@users.noreply.github.com>
Co-authored-by: Luciano Bello <bel@zurich.ibm.com>
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