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Home Page: https://mps9506.github.io/echor/
License: Other
Download EPA ECHO data in R
Home Page: https://mps9506.github.io/echor/
License: Other
Per emails from Hadley and CRAN, the new version of tidyr (v1.0.0) breaks the package.
https://tidyr.tidyverse.org/dev/news/index.html#breaking-changes
Looks like the vignette is the only thing that needs changing.
using urlEncode
in queryList
to build api argument calls breaks the way the list is built. URLencode
needs to be applied only to the list values so the function can properly paste each value into the string.
The nested tibble from downloadDMRs()
relies on the user mapping column types to unnest the dmr column:
library(dplyr)
library(echor)
df <- tibble::tibble(permit = c("TX0021474", "TX0023051", "TXG130053"))
df <- downloadDMRs(df, idColumn = permit, start_date = "01/01/2010",
end_date = "12/30/2017", parameter_code = "50050")
df %>% tidyr::unnest(dmr)
Results in the following message:
Error: Column `monitoring_location_code` can't be converted from character to numeric
I have to follow up with the following to unnest the data:
df %>%
mutate(n = purrr::map(dmr, ~nrow(.))) %>%
mutate(dmr = purrr::map(dmr, ~mutate(.x,
version_nmbr = as.character(version_nmbr),
monitoring_location_code = as.character(monitoring_location_code),
exceedence_pct = as.character(exceedence_pct),
rnc_detection_date = as.character(rnc_detection_date),
rnc_resolution_code = as.character(rnc_resolution_code),
rnc_resolution_date = as.character(rnc_resolution_date),
days_late = as.character(days_late),
nodi_code = as.character(nodi_code),
dmr_value_nmbr = as.numeric(dmr_value_nmbr),
dmr_value_standard_units = as.numeric(dmr_value_standard_units),
limit_value_nmbr = as.numeric(limit_value_nmbr),
limit_value_standard_units = as.numeric(limit_value_standard_units)))) %>%
tidyr::unnest(dmr)
The user should not have to figure this out, but if the above code is hardcoded, it will be prone to breaking if the columns returned by the API ever change.
ECHO's data service URLs are changing. Please update your code and bookmarks as soon as possible to maintain access to ECHO data. Users will need to adjust their URLs to start with https://echodata.epa.gov instead of https://ofmpub.epa.gov. The service documentation listed below has been changed to use the new URL.
Documentation and description need to be cleaned up and completed.
ggmap is included in suggests since it is used in the vignette. However, it is listed as an orphaned package and raises a note when checking as cran.
Prepare for release:
git pull
urlchecker::url_check()
devtools::check(remote = TRUE, manual = TRUE)
devtools::check_win_devel()
rhub::check_for_cran()
cran-comments.md
git push
Submit to CRAN:
usethis::use_version('patch')
devtools::submit_cran()
Wait for CRAN...
usethis::use_github_release()
This is to sort out functional issues required for fixing #79 .
I didn't realize getDownload endpoint restricts downloads to 100,000 rows. I used this endpoint because it returns a really convenient CSV file. The getQID endpoint returns all rows, but are paginated.
Possible approaches:
I'm planning on adopting the first approach.
getQID()
endpoint with url endpoint for each of the services.getQID()
to echoWaterGetFacilityInfo()
, echoAirGetFacilityInfo()
, and echoSDWGetSystems()
getGeoJSON()
call.Explore using https://github.com/SymbolixAU/geojsonsf to convert geojson to sf instead of st_read. Would eliminate the heavy dependency on sf.
the various *GetFacilityInfo() functions need an argument to specify which columns are returned.
Should provide sensible defaults.
Returning simple features is causing problems:
> x <- echoAirGetFacilityInfo(xmin = '-96.407563',
+ ymin = '30.554395',
+ xmax = '-96.25947',
+ ymax = '30.751984',
+ output = 'sf')
Request failed [500]. Retrying in 1 seconds...
Request failed [500]. Retrying in 2.6 seconds...
There was a server error, try again later.
Error: No 'type' member at object index 0 - invalid GeoJSON
Need a more flexible way of handling data returned by echoGetCAAPR
. Currently fails if the full record of data is not returned by ECHO.
Github Actions rendered readme and pkgdown has encoding errors in the in code box. eg:
library(echor)
## echoWaterGetFacilityInfo() will return a dataframe or simple features (sf) dataframe.
df <- echoWaterGetFacilityInfo(output = "df",
xmin = '-96.387509',
ymin = '30.583572',
xmax = '-96.281422',
ymax = '30.640008',
p_ptype = "NPD")
head(df)
#> �[90m# A tibble: 3 x 26�[39m
#> CWPName SourceID CWPStreet CWPCity CWPState CWPStateDistrict CWPZip
#> �[3m�[90m<chr>�[39m�[23m �[3m�[90m<chr>�[39m�[23m �[3m�[90m<chr>�[39m�[23m �[3m�[90m<chr>�[39m�[23m �[3m�[90m<chr>�[39m�[23m �[3m�[90m<chr>�[39m�[23m �[3m�[90m<chr>�[39m�[23m
#> �[90m1�[39m CENTRA… TX00027… 222 IREL… COLLEG… TX 09 77843
#> �[90m2�[39m HEAT T… TX01065… 0.25MI S… COLLEG… TX 09 77845
#> �[90m3�[39m TURKEY… TX00624… 3000FT W… BRYAN TX 09 77807
#> �[90m# … with 19 more variables: MasterExternalPermitNmbr �[3m�[90m<chr>�[90m�[23m, RegistryID �[3m�[90m<chr>�[90m�[23m,�[39m
#> �[90m# CWPCounty �[3m�[90m<chr>�[90m�[23m, CWPEPARegion �[3m�[90m<chr>�[90m�[23m, FacDerivedHuc �[3m�[90m<chr>�[90m�[23m, FacLat �[3m�[90m<dbl>�[90m�[23m,�[39m
#> �[90m# FacLong �[3m�[90m<dbl>�[90m�[23m, CWPTotalDesignFlowNmbr �[3m�[90m<dbl>�[90m�[23m,�[39m
#> �[90m# CWPActualAverageFlowNmbr �[3m�[90m<dbl>�[90m�[23m, ReceivingMs4Name �[3m�[90m<chr>�[90m�[23m,�[39m
#> �[90m# AssociatedPollutant �[3m�[90m<chr>�[90m�[23m, MsgpPermitType �[3m�[90m<chr>�[90m�[23m, CWPPermitStatusDesc �[3m�[90m<chr>�[90m�[23m,�[39m
#> �[90m# CWPPermitTypeDesc �[3m�[90m<chr>�[90m�[23m, CWPIssueDate �[3m�[90m<date>�[90m�[23m, CWPEffectiveDate �[3m�[90m<date>�[90m�[23m,�[39m
#> �[90m# CWPExpirationDate �[3m�[90m<date>�[90m�[23m, CWPSNCStatusDate �[3m�[90m<date>�[90m�[23m, StateAuthGen �[3m�[90m<chr>�[90m�[23m�[39m
If you query a large area that returns many values, ECHO returns a cluster with associated qid. The clusters break functional returns for users and do not provide useful info, in my opinion. The qid can be used to retrieve plant info using /cwa_rest_services.get_download
Need to modify echoWaterGetFacilityInfo()
to handle clusters, then pass a query using the qid with new function that calls cwa_res_services.get_download on EPA ECHO.
I also need to figure out the best practice to inform users that the function is returning one or the other.
Some new errors on CRAN:
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 310-315 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Expecting '}'
--- failed re-building 'introduction.Rmd'
SUMMARY: processing the following file failed:
'introduction.Rmd'
Error: Vignette re-building failed.
Execution halted
The example in the readme and vignette are returning empty dataframes.
please write package names and software names in single quotes (e.g. 'ECHO') in title and description.
Please explain all acronyms (e.g. EPA) in your description to avoid misunderstandings.
Please replace \dontrun{} by \donttest{} or unwap the examples if they can be executed in less than 5 sec per Rd-file.
Fix and resubmit.
To simplify functions for users, we can use a single function to call echoAirGetFacilityInfo()
, echoWaterGetFacilityInfo()
and echoSDWGetFacilityInfo()
.
For example:
echoGetFacilities(program = "caa", output = "df", ...)
Same for echoGetCAAPR()
and echoGetEffluent()
:
echoGetReports(program = "caa", p_id = "xyz", ...)
Need a good readme.
/cwa_rest_services.metadata provides metadata returned as JSON.
This would be prudent to add so users can look up metadata in R without having to link to webpages to find relevant info.
The following checks don't pass (https://cloud.r-project.org/web/checks/check_results_echor.html)
using R version 3.6.0 (2019-04-26)
using platform: x86_64-apple-darwin15.6.0 (64-bit)
using session charset: UTF-8
checking for file ‘echor/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘echor’ version ‘0.1.3’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘echor’ can be installed ... [4s/4s] OK
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... OK
checking whether the package can be loaded with stated dependencies ... OK
checking whether the package can be unloaded cleanly ... OK
checking whether the namespace can be loaded with stated dependencies ... OK
checking whether the namespace can be unloaded cleanly ... OK
checking loading without being on the library search path ... OK
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘lubridate’
All declared Imports should be used.
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [3s/4s] OK
checking Rd files ... OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [1s/1s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [2s/2s] OK
Running ‘testthat.R’ [1s/1s]
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking running R code from vignettes ... NONE
checking re-building of vignette outputs ... [3s/23s] OK
checking PDF version of manual ... OK
DONE
Status: 1 NOTE
check_spelling
seems to cause issues in build test:
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, :
PCDATA invalid Char value 27 [9]
Calls: <Anonymous> ... xml_find_all -> <Anonymous> -> read_xml.character -> read_xml.raw
Execution halted
Might be best to remove it and run spellchecks manually when writing documentation and vignettes.
No hurry as it won't cause warnings to end users yet. But could you please look into using dots_list()
or list2()
instead?
Running tests on new functions echoGetCAAPR
raises following notes:
checking R code for possible problems ... NOTE
echoGetCAAPR: no visible binding for global variable 'Year'
echoGetCAAPR: no visible binding for global variable 'Discharge'
echoGetCAAPR: no visible binding for global variable 'Year1'
echoGetCAAPR: no visible binding for global variable 'Year10'
Undefined global functions or variables:
Discharge Year Year1 Year10
Probably due to using dplyr and tidyr in this function.
Consider doing this with base R methods or understand how to use these undefined variables.
The dataframe returned by echoGetEffluent
has list within a list. Ideally, a clean dataframe/tibble should be returned. It might be better to call download_effluent_chart with this function.
Impacted examples:
echoWaterGetFacilityInfo()
Long batch processing jobs can fail when connection is reset by peer. Error occurs in curl_fetch_memory call -- this may be a curl issue, or this may be handleable in this module, unsure which is the approach. I am going to look into the code herein to see if another approach exists that can handle resets gracefully.
Error in curl::curl_fetch_memory(url, handle = handle) :
SSL read: error:00000000:lib(0):func(0):reason(0), errno 104
Calls: echoGetEffluent ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Prepare for release:
git pull
devtools::build_readme()
urlchecker::url_check()
devtools::check(remote = TRUE, manual = TRUE)
devtools::check_win_devel()
rhub::check_for_cran()
cran-comments.md
git push
Submit to CRAN:
usethis::use_version('patch')
devtools::submit_cran()
Wait for CRAN...
git push
usethis::use_github_release()
usethis::use_dev_version()
git push
Suggest using progress.
Do I want to import this for one function?
no matter what qcolumns are specified, echo always provides columns 1 and 2.
Need to do some list matching to see if the user includes 1 and 2 in the q columns list, and always include 1 and 2 in the col_types argument...
Documentation is thin, but there are a bunch of new endpoints here:
https://echo.epa.gov/tools/web-services/loading-tool
A helper function to using purrr::map
to download DMR effluent reports would be useful since we can only download one at a time. Something like:
df <- tibble(PermitId = c("TX0021474", "TX0023051", "TXG130053"))
# create the progress bar with a dplyr function.
pb <- progress_estimated(length(df$PermitId))
df <- df %>%
mutate(reports = purrr::pmap(., ~ {
# update the progress bar (tick()) and print progress (print())
pb$tick()$print()
echoGetEffluent(
p_id = ..2,
parameter = "50050",
start_date = "01/01/2008",
end_date = "12/30/2017")
}
))
Concerns: Might be ripe for abusive behavior of ECHO server.
MWE doesn't work:
df <- data_frame("p_id" = c('TX0119407', 'TX0132187', 'TX040237'))
df <- downloadDMRs(df, p_id)
Error in echoGetEffluent(p_id = ..1, ...) :
formal argument "p_id" matched by multiple actual arguments
Also on CRAN an additional issue list:
* checking examples with --run-donttest ... [3s/27s] ERROR
Running examples in ‘echor-Ex.R’ failed
The error most likely occurred in:
> ### Name: echoGetCAAPR
> ### Title: Download EPA ECHO emissions inventory report data
> ### Aliases: echoGetCAAPR
>
> ### ** Examples
>
> ## No test:
> ## This example requires an internet connection to run
>
> echoGetCAAPR(p_id = '110000350174')
Error: Can't subset columns that don't exist.
✖ Column `Year1` doesn't exist.
Backtrace:
█
1. └─echor::echoGetCAAPR(p_id = "110000350174")
2. ├─tidyr::gather_(...)
3. └─tidyr:::gather_.data.frame(...)
4. ├─tidyr::gather(...)
5. └─tidyr:::gather.data.frame(...)
6. ├─base::unname(tidyselect::vars_select(tbl_vars(data), !!!quos))
7. └─tidyselect::vars_select(tbl_vars(data), !!!quos)
8. └─tidyselect:::eval_select_impl(...)
9. ├─tidyselect:::with_subscript_errors(...)
10. │ ├─base::tryCatch(...)
11. │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
12. │ │ └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. │ │ └─base:::doTryCatch(return(expr), name, parentenv, handler)
14. │ └─tidyselect:::instrument_base_errors(expr)
15. │ └─base::withCallingHand
Execution halted
Write new tests for:
echoGetCAAPR
echoAirGetFacilityInfo
I'm having trouble running queries that return more than 100k results. For example, when I run the following:
facilities <-
echoWaterGetFacilityInfo(output = 'df',
qcolumns = "1",
p_st = "GA")
I get a dataframe that looks like this:
Is this expected behavior?
What seems like is happening is that the original query has a result set of around 122k records, and the get_download
endpoint returns an error when requesting a result of more than 100k records. Trying this query directly via the ECHO Swagger:
https://echodata.epa.gov/echo/cwa_rest_services.get_download?output=CSV&qid=MY_QUERY_ID&qcolumns=1
I get the following:
<b>FILE OUTPUT FAILED</b>
<br />
<b>ERROR MESSAGE:</b> This query of 122923 exceeds the maximum rows allowed for a download of 100000. Please modify your selection.
I think what should happen in this case is that echor should fall back to using the get_qid
endpoint, which seems to allow pagination.
Functions are erroring on HTTP 500 and not returning a "graceful" message instead of error or warning.
* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/echor.Rcheck’
* using R Under development (unstable) (2023-06-12 r84534)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
* running under: Fedora 34 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘echor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘echor’ version ‘0.1.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘echor’ can be installed ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [2s/18s] ERROR
Running examples in ‘echor-Ex.R’ failed
The error most likely occurred in:
> ### Name: echoAirGetFacilityInfo
> ### Title: Downloads EPA ECHO permitted air emitter information
> ### Aliases: echoAirGetFacilityInfo
>
> ### ** Examples
>
> ## No test:
> ## These examples require an internet connection to run
>
> ## Retrieve table of facilities by bounding box
> echoAirGetFacilityInfo(xmin = '-96.407563',
+ ymin = '30.554395',
+ xmax = '-96.25947',
+ ymax = '30.751984',
+ output = 'df')
# A tibble: 40 × 7
AIRName SourceID AIRStreet AIRCity AIRState FacLat FacLong
<chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
1 AGGIE CLEANERS 0600000… 111 COLL… COLLEG… TX 30.6 -96.3
2 ALENCO, DIV OF RELIANT BL… TX00000… 615 CARS… BRYAN TX 30.6 -96.4
3 ALL SEASONS 1 HR CLEANERS 0600000… 2501 TEX… COLLEG… TX 30.6 -96.3
4 BLUEBONNET PAVING TX00000… HWY. 60,… COLLEG… TX 30.6 -96.3
5 BRIARCREST DRY CLEANERS 0600000… 1887 BRI… BRYAN TX 30.7 -96.3
6 BRYAN CERAMICS PLANT TX00000… 1500 IND… BRYAN TX 30.7 -96.4
7 BRYAN CLEANERS & LAUNDRY 0600000… 1803 HOL… COLLEG… TX 30.6 -96.3
8 BRYAN HICKS GAS PLANT TX00000… 3747 OLD… BRYAN TX 30.7 -96.3
9 CITGO PETROLEUM CORPORATI… TX00000… 1714 FIN… BRYAN TX 30.7 -96.4
10 CITY OF BRYAN TX00000… 1.5 MI W… BRYAN TX 30.6 -96.4
# ℹ 30 more rows
>
> ## Retrieve a simple features dataframe by bounding box
> spatialdata <- echoAirGetFacilityInfo(xmin = '-96.407563',
+ ymin = '30.554395',
+ xmax = '-96.25947',
+ ymax = '30.751984',
+ output = 'sf')
Request failed [500]. Retrying in 1 seconds...
Request failed [500]. Retrying in 1.5 seconds...
Error in resp_check(request) : Internal Server Error (HTTP 500).
Calls: echoAirGetFacilityInfo -> getGeoJson -> resp_check -> stop_for_status
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE
Status: 1 ERROR
See
‘/data/blackswan/ripley/R/packages/tests-devel/echor.Rcheck/00check.log’
for details.
Command exited with non-zero status 1
Time 0:55.23, 32.75 + 5.62
Prepare for release:
devtools::build_readme()
devtools::check(remote = TRUE, manual = TRUE)
devtools::check_win_devel()
rhub::check_for_cran(env_vars = c(R_CHECK_FORCE_SUGGESTS = "true", R_CHECK_CRAN_INCOMING_USE_ASPELL = "true", R_COMPILE_AND_INSTALL_PACKAGES = "always"), platforms = c("windows-x86_64-release", "windows-x86_64-devel", "macos-highsierra-release-cran")
revdepcheck::revdep_check(num_workers = 4)
cran-comments.md
Submit to CRAN:
usethis::use_version('patch')
devtools::submit_cran()
Wait for CRAN...
usethis::use_github_release()
usethis::use_dev_version()
Prepare for release:
git pull
urlchecker::url_check()
devtools::check(remote = TRUE, manual = TRUE)
devtools::check_win_devel()
rhub::check_for_cran()
cran-comments.md
git push
Submit to CRAN:
usethis::use_version('patch')
devtools::submit_cran()
Wait for CRAN...
git push
usethis::use_github_release()
git push
Prepare for release:
devtools::build_readme()
urlchecker::url_check()
devtools::check(remote = TRUE, manual = TRUE)
devtools::check_win_devel()
rhub::check_for_cran()
revdepcheck::revdep_check(num_workers = 4)
cran-comments.md
Submit to CRAN:
usethis::use_version('patch')
devtools::submit_cran()
Wait for CRAN...
usethis::use_github_release()
usethis::use_dev_version()
Check raises:
Malformed Description field: should contain one or more complete sentences.
Should be easy fix.
The effluent endpoint returns multipage data when more than 100,000 records are returned. The SDW endpoints return an error when more than 100,000 records are returned:
curl -X GET "https://echodata.epa.gov/echo/sdw_rest_services.get_systems?p_st=CA%2CGA%2CFL%2COH%2COR%2CTX%2CVA%2CWA" -H "accept: application/json"
{
"Results": {
"Error": {
"ErrorMessage": "Rows Returned would be 101380. Queryset Limit would be exceeded - please make search parameters more selective."
}
}
}
the get_download endpoint still returns a full csv for <100,000 rows. Would make sense return a message when queryset is exceeded and remove the code for parsing pages returned by get_qid endpoint.
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