Add Spell Checker #103

bpaul4 · 2024-04-09T18:15:54Z

Add Spell Checker

Fixes #102

{Description}

Add CI check on spelling for Python files, documentation and general text files
Adds common exceptions (e.g., "IDAES", hexadecimal keys, ...) and fixes a small batch of typos

Legal Acknowledgement

By contributing to this software project, I agree to the following terms and conditions for my contribution:

I agree my contributions are submitted under the license terms described in the LICENSE.txt file at the top level of this directory.
I represent I am authorized to make the contributions and grant the license. If my employer has rights to intellectual property that includes these contributions, I represent that I have received permission to make contributions and grant the required license on behalf of that employer.

…to spelling

andrewlee94 · 2024-04-12T16:22:11Z

@bpaul4 I went throguh and fixed most/all of the typos in the idaes-examples/mod folder.

ksbeattie · 2024-04-13T01:14:33Z

I just pushed a bunch of changes, one commit per "correction". Please, more knowledgeable people, review.

FWIW, here's an example of how I did the individual "search and replace" via the macos command line:

sed -i '~' 's/intialization/initialization/g' $(grep -rl intialization)

Edit: Use the w option in the grep here if you want correction to be on a word boundary. It may not always be what is needed but it helps in situations where the misspelled word is part of another correctly spelled word, like:

sed -i '~' 's/compressio/compressor/g' $(grep -rwl compressio)

bpaul4 · 2024-04-15T13:40:02Z

Thanks @ksbeattie, your commits look good and the regenerated SVG files look good as well. The "search and replace" is an interesting tool to have, can this be done on Windows as well?

lbianchi-lbl · 2024-04-25T19:42:16Z

@bpaul4 After looking at the notebook where the pandas warnings are causing the spellcheck to fail, I think the code that causes the warnings to be emitted may actually be in the notebook itself, even though the word being flagged as a misspelling (ser) is defined elsewhere (most likely within pandas):

So, applying the suggested fix (using float(data["my_column"].iloc[0]) instead of float(data["my_column"])) should cause the warnings, and consequently those spellcheck failures, to go away.

bpaul4 · 2024-04-25T20:18:44Z

@agarciadiego in the image above from the notebook "Using Parameter Estimation with Modular Property Packages", it appears that in some variables are set to values of float(a dictionary value) and some expressions are defined as float(a dictionary series) - a_model_variable. Would you be able to investigate which are causing the FutureWarnings and push any syntax corrections to this PR?

lbianchi-lbl · 2024-04-25T23:53:30Z

@agarciadiego in the image above from the notebook "Using Parameter Estimation with Modular Property Packages", it appears that in some variables are set to values of float(a dictionary value) and some expressions are defined as float(a dictionary series) - a_model_variable. Would you be able to investigate which are causing the FutureWarnings and push any syntax corrections to this PR?

@bpaul4 @agarciadiego I've created a dedicated issue to track this separately from this PR: #108.

See IDAES#108

lbianchi-lbl · 2024-04-26T00:09:43Z

The spellcheck is now passing, however the notebooks tests are failing because of an AssertionError in active/power_gen/ngcc/ngcc_test.ipynb:

I was able to confirm the same failure running locally (Ubuntu 20.04, Python 3.10.14).

Any thoughts on how likely it is that the failure is related to the changes in this PR?

lbianchi-lbl · 2024-04-26T00:46:11Z

Update: I ran git bisect between 5703f2a (bad) and f62f20f (good) using git bisect run bash -c 'pytest --verbose idaes_examples/notebooks/active/power_gen/ ; status=$? ; git reset --hard ; exit $status' as a "probe". According to this, the commit that introduced the failure is 4b805f3:

4b805f3f04a67e37e0cf3f228d7cdb53a7bdf86d is the first bad commit
commit 4b805f3f04a67e37e0cf3f228d7cdb53a7bdf86d
Author: Andrew Lee <[email protected]>
Date:   Fri Apr 12 12:20:16 2024 -0400

    Fixing typos in idaes_examples/mod

 .../NETL_32D_gas_phase_thermo.py                   |  6 +++---
 .../NETL_32D_solid_phase_thermo.py                 |  6 +++---
 idaes_examples/mod/dae/petsc/pid_steam_tank.py     |  4 ++--
 idaes_examples/mod/hda/hda_ideal_VLE.py            | 14 +++++++-------
 idaes_examples/mod/methanol/methanol_param_VLE.py  |  4 ++--
 .../mod/methanol/methanol_state_block_VLE.py       |  6 +++---
 idaes_examples/mod/power_gen/SOFC_ROM.py           |  2 +-
 idaes_examples/mod/power_gen/gas_turbine.py        | 22 +++++++++++-----------
 idaes_examples/mod/power_gen/hrsg.py               |  4 ++--
 idaes_examples/mod/power_gen/ngcc.py               |  8 ++++----
 idaes_examples/mod/power_gen/ngcc_soec_costing.py  |  4 ++--
 idaes_examples/mod/power_gen/soec.py               |  6 +++---
 .../properties/thermophysical_property_example.py  |  6 +++---
 13 files changed, 46 insertions(+), 46 deletions(-)
bisect run success

I see that this commit doesn't directly affect the failing notebook idaes_examples/notebooks/active/power_gen/ngcc/ngcc_test.ipynb, but it does make some functional (in the sense of "not non-functional") changes to Python modules in idaes_examples/mod/power_gen, which, based on the naming alone, makes me think they might be related. Any idea on what might be happening?

JavalVyas2000 · 2024-04-26T00:59:07Z

idaes_examples/mod/power_gen/gas_turbine.py
idaes_examples/mod/power_gen/hrsg.py
idaes_examples/mod/power_gen/ngcc.py

The above are the files used in ngcc flowsheet. I will look into this and let you know.

JavalVyas2000 · 2024-04-26T01:12:57Z

The commit commit changes a variable name and the model is being initialized from a saved solution which has the incorrect spelling for cap_additional_co2 and I believe this is a reason why there is an assert error.

lbianchi-lbl · 2024-04-26T01:55:52Z

Thanks @JavalVyas2000 for the tip. I was able to delete the outdated ngcc_init.json.gz and re-run the notebook locally, which resulted in a new file with up-to-date variables being created. All checks are now passing.

bpaul4 · 2024-04-26T13:07:04Z

Thank you @andrewlee94 @ksbeattie @JavalVyas2000 @lbianchi-lbl for your contributions to this PR. It looks like everything is passing now and all spelling/other issues have been resolved.

lbianchi-lbl

Thanks @bpaul4 for leading this effort!

agarciadiego

LGTM

bpaul4 · 2024-04-26T13:23:55Z

@andrewlee94 do you have any further suggestions or requests before we merge this?

andrewlee94 · 2024-04-26T13:45:40Z

pyproject.toml

+# Ignore Attemp - assume it is abbreviating attemperator
+Attemp = "Attemp"
+# Ignore ba in hexadecimal values, or block names
+ba = "ba"


Is this ignore still required now that we have the regex later to exclude the hex values in the id field? If not, we should remove it.

I think it might still be needed, it's quick to test though so I'll do that now.

Tested locally, it catches block names e.g. ba23 and also atomic element usage of Ba for barium. Those are flagged as typos if this ignore line is taken out.

First, where is ba23 used? That does not look like a very good name for a block.
Catching Ba for barium is important, but we should update the comment to indicate this.

When the exception is removed, these typos are flagged:

(all-installed-3.9) C:\Users\Brandon\GitHub\IDAES\examples>typos error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:345:594 | 345 | " <text xml:space=\"preserve\" style=\"font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:2.11667px;line-height:1.25;font-family:sans-serif;-inkscape-font-specification:'sans-serif, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;text-align:center;text-anchor:middle;stroke-width:0.264583\" x=\"21.494312\" y=\"157.50975\" id=\"text962-24-7-1-8-9-9-45-7-5-5-8-4-5\"><tspan sodipodi:role=\"line\" id=\"tspan39444\" x=\"21.494312\" y=\"157.50975\" style=\"font-weight:bold\">ba00</tspan></text>\n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:403:606 | 403 | " <text xml:space=\"preserve\" style=\"font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:2.11667px;line-height:1.25;font-family:sans-serif;-inkscape-font-specification:'sans-serif, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;text-align:center;text-anchor:middle;stroke-width:0.264583\" x=\"70.442276\" y=\"117.82269\" id=\"text962-24-7-1-8-9-9-45-7-5-5-8-4-5-9-8-0\"><tspan sodipodi:role=\"line\" id=\"tspan39444-3-1-3\" x=\"70.442276\" y=\"117.82269\" style=\"font-weight:bold\">ba03</tspan></text>\n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:409:409 | 409 | " <text xml:space=\"preserve\" style=\"font-style:normal;font-weight:normal;font-size:2.11667px;line-height:1.25;font-family:sans-serif;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.264583\" x=\"42.142143\" y=\"151.60056\" id=\"text29235\"><tspan sodipodi:role=\"line\" id=\"tspan29233\" style=\"font-size:2.11667px;stroke-width:0.264583;font-weight:bold\" x=\"42.142143\" y=\"151.60056\">ba01</tspan></text>\n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:411:413 | 411 | " <text xml:space=\"preserve\" style=\"font-style:normal;font-weight:normal;font-size:2.11667px;line-height:1.25;font-family:sans-serif;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.264583\" x=\"42.671307\" y=\"123.55508\" id=\"text29235-4\"><tspan sodipodi:role=\"line\" id=\"tspan29233-1\" style=\"font-size:2.11667px;stroke-width:0.264583;font-weight:bold\" x=\"42.671307\" y=\"123.55508\">ba02</tspan></text>\n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1043:19 | 1043 | " <th>ba00</th>\n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1063:19 | 1063 | " <th>ba01</th>\n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1083:19 | 1083 | " <th>ba02</th>\n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1103:19 | 1103 | " <th>ba03</th>\n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1916:9 | 1916 | "ba00 68.682089 2380.214335 56.279763 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1917:9 | 1917 | "ba01 68.682089 2380.214335 48.360706 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1918:9 | 1918 | "ba02 15.392573 480.796393 9.768722 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1919:9 | 1919 | "ba03 15.392573 480.796393 13.562943 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1969:9 | 1969 | "ba00 288.150000 1.013250e+05 0.0092 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1970:9 | 1970 | "ba01 310.930000 1.272390e+05 0.0092 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1971:9 | 1971 | "ba02 310.930000 1.272390e+05 0.003065 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_flowsheet.py:228:8 | 228 | fs.ba01 = Arc(source=fs.intercooler_s2.outlet, destination=fs.ASU.inlet) | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:1972:9 | 1972 | "ba03 431.696780 1.272390e+05 0.003065 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_flowsheet.py:271:8 | 271 | fs.ba02 = Arc(source=fs.ASU.O2_outlet, destination=fs.oxygen_preheater.tube_inlet) | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2022:9 | 2022 | "ba00 0.0003 0.0099 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_flowsheet.py:363:8 | 363 | fs.ba03 = Arc( | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2023:9 | 2023 | "ba01 0.0003 0.0099 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2024:9 | 2024 | "ba02 0.0 0.0 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2025:9 | 2025 | "ba03 0.0 0.0 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2075:9 | 2075 | "ba00 0.7732 0.2074 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_flowsheet.py:1515:30 | 1515 | iinit.propagate_state(fs.ba01) | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2076:9 | 2076 | "ba01 0.7732 0.2074 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_flowsheet.py:1517:30 | 1517 | iinit.propagate_state(fs.ba02) | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2077:9 | 2077 | "ba02 0.001914 0.995021 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_flowsheet.py:1521:30 | 1521 | iinit.propagate_state(fs.ba03) | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2078:9 | 2078 | "ba03 0.001914 0.995021 0.0 0.0 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_flowsheet.py:1887:14 | 1887 | "ba00": fs.air_compressor_s1.inlet, | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2128:9 | 2128 | "ba00 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_flowsheet.py:2048:14 | 2048 | "ba00": fs.air_compressor_s1.inlet, | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2129:9 | 2129 | "ba01 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2130:9 | 2130 | "ba02 \n", | ^^ | error: `ba` should be `by`, `be` --> .\idaes_examples\archive\power_gen\rsofc\rsofc_soec_src.ipynb:2131:9 | 2131 | "ba03 0.0 0.0 \n", | ^^ | error: `Ba` should be `By`, `Be` --> .\idaes_examples\archive\matopt\metal_oxide_bulk_design_src.ipynb:117:22 | 117 | "Atoms = [Atom(\"Ba\"), Atom(\"Fe\"), Atom(\"In\"), Atom(\"O\")]" | ^^ | error: `Ba` should be `By`, `Be` --> .\idaes_examples\archive\matopt\metal_oxide_bulk_design_src.ipynb:225:169 | 225 | "For this system, we introduce several rules about the allowed placement of atoms in the design. First, we require that all A-sites in the material are occupied by Ba. Next, we require that all O-sites are occupied by O. Thirdly, we forbid Ba and O from being placed in B-sites. And finally, we require that some atom be placed in each B-site. These four rules effectively limit the scope of the optimization to focus on the labeling of B-sites as either Fe or In. " | ^^ | error: `Ba` should be `By`, `Be` --> .\idaes_examples\archive\matopt\metal_oxide_bulk_design_src.ipynb:225:245 | 225 | "For this system, we introduce several rules about the allowed placement of atoms in the design. First, we require that all A-sites in the material are occupied by Ba. Next, we require that all O-sites are occupied by O. Thirdly, we forbid Ba and O from being placed in B-sites. And finally, we require that some atom be placed in each B-site. These four rules effectively limit the scope of the optimization to focus on the labeling of B-sites as either Fe or In. " | ^^ | error: `Ba` should be `By`, `Be` --> .\idaes_examples\archive\matopt\metal_oxide_bulk_design_src.ipynb:234:69 | 234 | "m.Yik.rules.append(FixedTo(1, sites=ASites, site_types=[Atom(\"Ba\")]))\n", | ^^ | error: `Ba` should be `By`, `Be` --> .\idaes_examples\archive\matopt\metal_oxide_bulk_design_src.ipynb:236:69 | 236 | "m.Yik.rules.append(FixedTo(0, sites=BSites, site_types=[Atom(\"Ba\"), Atom(\"O\")]))\n", | ^^ | error: `Ba` should be `By`, `Be` --> .\idaes_examples\archive\matopt\metal_oxide_bulk_design_src.ipynb:246:342 | 246 | "Notice that in each case, we specify a subset of locations or atoms of interest. This is because, for example, our material activity depends on oxygen sites only and it would be nonsensical to try to interpret one of the conformations on a different type of site. Similarly, the dopant budgets are written only over In atoms and not on Ba, Fe, or O. " | ^^ | error: `Ba` should be `By`, `Be` --> .\idaes_examples\archive\matopt\metal_oxide_bulk_design.py:32:20 | 32 | Atoms = [Atom('Ba'), Atom('Fe'), Atom('In'), Atom('O')] | ^^ | error: `Ba` should be `By`, `Be` --> .\idaes_examples\archive\matopt\metal_oxide_bulk_design.py:54:67 | 54 | m.Yik.rules.append(FixedTo(1, sites=ASites, site_types=[Atom('Ba')])) | ^^ | error: `Ba` should be `By`, `Be` --> .\idaes_examples\archive\matopt\metal_oxide_bulk_design.py:56:67 | 56 | m.Yik.rules.append(FixedTo(0, sites=BSites, site_types=[Atom('Ba'), Atom('O')]))

OK - we should update the comment however to indicate that it is there to catch these (as otherwise someone else might as k the same question I did).

bpaul4 added 2 commits April 9, 2024 10:30

CI framework for spell check test

7725c44

fix some typos

4c4c7e0

ksbeattie added the Priority:Normal Normal Priority Issue or PR label Apr 11, 2024

ksbeattie assigned ksbeattie, bpaul4, JavalVyas2000 and andrewlee94 Apr 11, 2024

andrewlee94 added 2 commits April 12, 2024 12:20

Fixing typos in idaes_examples/mod

4b805f3

Merge branch 'spell-checker' of https://github.com/bpaul4/examples in…

2df72cc

…to spelling

andrewlee94 and others added 18 commits April 12, 2024 12:25

Fixing some missed typos

516509c

Fixing more typos

8751550

Adding a couple of exclusions

85b062f

documentaiton should be documentation

198b519

varaibles should be variables

96ba049

algebriac to algebraic

dfa5019

relase should be release

4246adb

whcih should be which

96ab158

addtional should be additional

06ca417

upadate should be update

dc61ba5

deafault should be default

f5626ab

indepedent should be independent

3510eca

convienience should be convenience

c3b15d8

memeory should be memory

2781743

desriptors should be descriptors

fe65eed

Curent should be Current

c3b0603

coversion should be conversion

1f8c0b2

intialization should be initialization

5874218

ksbeattie requested a review from lbianchi-lbl April 25, 2024 18:56

Remove RIPE example exceptions

3f29630

bpaul4 requested a review from agarciadiego April 25, 2024 20:15

lbianchi-lbl added 6 commits April 25, 2024 18:36

Merge branch 'main' into spell-checker

cee47bf

"Diagnositcs" should be "Diagnostics"

0f0963a

"maxmimum" should be "maximum"

7054188

"discrepency" should be "discrepancy"

4f57f1f

"auxilaries" should be "auxiliaries"

2d37ba7

"Stream_lables_leader" should be "Stream_label_leader"

f401306

Add regex to exclude "ser" as it appears in pandas warnings

5703f2a

See IDAES#108

Try recreating the ngcc init file after changes in 4b805f3

028cacd

bpaul4 marked this pull request as ready for review April 26, 2024 13:07

bpaul4 requested a review from andrewlee94 April 26, 2024 13:07

lbianchi-lbl approved these changes Apr 26, 2024

View reviewed changes

agarciadiego approved these changes Apr 26, 2024

View reviewed changes

andrewlee94 reviewed Apr 26, 2024

View reviewed changes

Update "Ba" exception comment

3d4ef04

lbianchi-lbl enabled auto-merge (squash) April 26, 2024 14:36

lbianchi-lbl merged commit b4badf7 into IDAES:main Apr 26, 2024
8 checks passed

bpaul4 deleted the spell-checker branch October 1, 2024 14:29

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Add Spell Checker #103

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bpaul4 commented Apr 9, 2024 •

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ksbeattie commented Apr 13, 2024 •

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lbianchi-lbl commented Apr 25, 2024 •

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lbianchi-lbl commented Apr 25, 2024 •

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lbianchi-lbl commented Apr 26, 2024 •

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JavalVyas2000 commented Apr 26, 2024 •

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lbianchi-lbl commented Apr 26, 2024 •

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