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Merged
merged 113 commits into from
Mar 29, 2023
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4d04b19
add popsafe county -> fips and state data files
nmdefries Feb 16, 2023
b3a03d4
construct class attributes using CROSSWALK keys
nmdefries Feb 16, 2023
0284c28
support popsafe-fips in geomap.py; get_geos_within to take "fips"
nmdefries Feb 16, 2023
1f8a21b
combine fips and popsafe-fips get_geo_within logic; comments
nmdefries Feb 20, 2023
fb82be4
code to generate popsafe tables
nmdefries Feb 20, 2023
f284b91
document group assignment procedure
nmdefries Feb 21, 2023
ba62241
add lowpop county group mapping file
nmdefries Feb 21, 2023
a1c491c
test popsafe-fips
nmdefries Feb 20, 2023
f74aefd
linting
nmdefries Feb 21, 2023
6a60915
remove public-read ACL since we have a policy on the bucket
nmdefries Feb 22, 2023
8c31b5d
upload prediction files only
nmdefries Feb 23, 2023
dfc8f1c
capture aws cp message to check if files were uploaded successfully
nmdefries Feb 23, 2023
130aef3
Merge pull request #1798 from cmu-delphi/bot/sync-prod-main
krivard Feb 24, 2023
519868b
fix the bug for 02-29
Feb 27, 2023
b1d481f
Merge pull request #1799 from cmu-delphi/fix_bug_for_special_date
krivard Feb 27, 2023
96f2ecf
msg fn to concat automatically; replace str_interp with paste
nmdefries Feb 27, 2023
1202646
remove rlang pronouns for speed
nmdefries Feb 28, 2023
3a23c12
changed flash timeout
Feb 28, 2023
356d173
minor changes to runner to reflect issue with FlaSH timeout
Feb 28, 2023
d6c0465
Deactivate safegraph_patterns
minhkhul Feb 28, 2023
a6b370e
remove ansible files
minhkhul Feb 28, 2023
86e1163
remove unnecessary pipes and combine filters
nmdefries Feb 28, 2023
1ea75b9
Merge pull request #1801 from cmu-delphi/deactivate_safegraph_patterns
minhkhul Feb 28, 2023
ec9a30f
Merge pull request #1796 from cmu-delphi/ndefries/backfill/aws-upload…
krivard Mar 1, 2023
52f747a
perform data validation on dates-as-strings
nmdefries Mar 1, 2023
523b1a6
call validation once to reduce calls to "duplicate"
nmdefries Mar 1, 2023
0dd2c9d
use joins instead of merge
nmdefries Mar 2, 2023
849834e
remove test code
nmdefries Mar 2, 2023
1a1bba7
change code name
nmdefries Mar 2, 2023
bb7df1a
generate local county mapping from CHNG spreadsheet
nmdefries Mar 3, 2023
2906b3c
only run backfill corrections on states for now
nmdefries Mar 3, 2023
be8da31
remove "population" wording in relation to chng-fips
nmdefries Mar 3, 2023
54faa45
rename local county groups csv to not mention population
nmdefries Mar 3, 2023
ec480d2
Add
M5Skid Mar 9, 2023
8536c97
Update params template to suppress s05 errors
M5Skid Mar 9, 2023
bc6fdb0
Update prod params to suppress s05 errors
M5Skid Mar 9, 2023
40699ef
Updates to threading, FlaSH files pull from AWS instead of local
Ananya-Joshi Mar 10, 2023
e464530
removed jhu flash files (now they are pulled from AWS
Ananya-Joshi Mar 10, 2023
13babe4
added back two necessary files
Ananya-Joshi Mar 10, 2023
18a08a5
drop split-out county fields; don't always exist in input
nmdefries Mar 13, 2023
0ef6b13
split out single counties from fips_list field
nmdefries Mar 13, 2023
f9ed4d4
raise error if new groups seen
nmdefries Mar 13, 2023
4fa39b7
state_fips and group are already str; don't need to cast
nmdefries Mar 13, 2023
4b9e836
Merge branch 'ndefries/geomapper/popsafe-county-level' into ndefries/…
nmdefries Mar 13, 2023
b7f6a3e
keep ref date as string
nmdefries Mar 13, 2023
4924695
keep issue date as string
nmdefries Mar 13, 2023
2b6413d
change global and weekday flags from binary to floats
Ananya-Joshi Mar 13, 2023
4141aed
last csv file
Ananya-Joshi Mar 13, 2023
54a86a4
minor lint fix
Ananya-Joshi Mar 13, 2023
dc02bb5
make error more actionable
nmdefries Mar 13, 2023
a2623a7
added Dmitry's geo mapping solution to reduce the number of files
Ananya-Joshi Mar 13, 2023
b4caa58
Merge pull request #1802 from cmu-delphi/ndefries/backfill/speed
korlaxxalrok Mar 14, 2023
3d8b041
exponentiate and delete old preds in single step
nmdefries Mar 14, 2023
6a3ad5b
typo in log message
nmdefries Mar 14, 2023
f4fe384
drop extraneous pipes and dplyr imports
nmdefries Mar 14, 2023
b9009a4
specify format for all date conversions
nmdefries Mar 13, 2023
ed530f0
Merge pull request #1804 from cmu-delphi/ndefries/backfill/state-only
korlaxxalrok Mar 14, 2023
f785b22
Merge pull request #1803 from cmu-delphi/ndefries/geomapper/chng-fips…
korlaxxalrok Mar 14, 2023
3943bd4
Merge pull request #1787 from cmu-delphi/ndefries/geomapper/popsafe-c…
korlaxxalrok Mar 14, 2023
46a2fc3
notes on TODOs
nmdefries Mar 14, 2023
1b71f21
fill missing vals using a lower-level fn directly
nmdefries Mar 16, 2023
ca1d5a4
Merge pull request #1805 from M5Skid/google-symptoms-suppress
korlaxxalrok Mar 16, 2023
d4dc447
replace rollmeanr with faster, free license version
nmdefries Mar 16, 2023
e472033
use rcpproll to match zoo values with high precision
nmdefries Mar 16, 2023
78b9d85
make rcpproll faster by computing all means at once
nmdefries Mar 16, 2023
678a7e4
Merge branch 'ndefries/backfill/speed2' into ndefries/backfill/speed-…
nmdefries Mar 17, 2023
c1a9e10
use purrr::reduce instead of base::Reduce
nmdefries Mar 17, 2023
2976588
resolve TODOs
nmdefries Mar 17, 2023
5e9f659
fix date type in test
nmdefries Mar 20, 2023
d8c61e6
remove unnecessary direct package refs
nmdefries Mar 20, 2023
802d11b
Merge branch 'ndefries/backfill/speed2' into ndefries/backfill/speed-…
nmdefries Mar 20, 2023
226d591
parallelize loop over geos
nmdefries Mar 20, 2023
fdd1b5c
use bettermc parallel apply
nmdefries Mar 20, 2023
1684559
reduce messages
nmdefries Mar 21, 2023
a8694d7
default to using parallel mode in production
nmdefries Mar 21, 2023
b301361
no longer need zoo package
nmdefries Mar 21, 2023
00078fe
add params flag to toggle backfill file generation in quidel
nmdefries Mar 21, 2023
16d80e8
delete
minhkhul Mar 21, 2023
5e25f4a
add params flag to toggle backfill file generation in changehc
nmdefries Mar 21, 2023
d3cb4a9
add params flag to toggle backfill file generation in claims_hosp
nmdefries Mar 21, 2023
329d8c3
Merge pull request #1809 from cmu-delphi/cdc_covidnet-deactivation
minhkhul Mar 21, 2023
c73c197
linting
nmdefries Mar 21, 2023
0361649
add new arg in tests
nmdefries Mar 21, 2023
bdf6da8
deactivate hhs_facilities
minhkhul Mar 21, 2023
86e6b2e
Merge pull request #1811 from cmu-delphi/hhs_facilities-deactivation
minhkhul Mar 21, 2023
ab0b6f9
check lp_solver setting
nmdefries Mar 22, 2023
cd7c4c0
test lp_solver selection logic
nmdefries Mar 22, 2023
b964eb8
first documentation updates
Ananya-Joshi Mar 23, 2023
25c94fa
Update _delphi_utils_python/delphi_utils/flash_eval/eval_day.py
Ananya-Joshi Mar 23, 2023
24eef14
updated function documentation pt 2
Ananya-Joshi Mar 23, 2023
e8ec3dd
changes to runner wait & smaller test
Ananya-Joshi Mar 23, 2023
8550808
lint nit
Ananya-Joshi Mar 23, 2023
01f1d7a
changed filename to be compatible with eval day code
Ananya-Joshi Mar 23, 2023
023f54f
capture license expiration error
nmdefries Mar 22, 2023
6e859eb
fix evalday test
Ananya-Joshi Mar 23, 2023
dd94d35
final nits
Ananya-Joshi Mar 23, 2023
b793fe1
use glpk explicitly in tests; default to glpk if gurobi license missing
nmdefries Mar 23, 2023
8126b21
fuzzy check on expiration errors
nmdefries Mar 23, 2023
db55f08
list mockr as needed package
nmdefries Mar 23, 2023
e3daff2
check gurobi license validity only if lp_solver is gurobi
nmdefries Mar 23, 2023
44640a8
Revert "Google-Symptoms suppress s05 low export errors"
M5Skid Mar 24, 2023
cf5f1cb
Merge pull request #1813 from cmu-delphi/revert-1805-google-symptoms-…
krivard Mar 24, 2023
cad3600
Merge pull request #1806 from cmu-delphi/ndefries/backfill/speed-join…
krivard Mar 27, 2023
a065d3d
Merge pull request #1807 from cmu-delphi/ndefries/backfill/speed2
krivard Mar 27, 2023
b44e22c
Merge pull request #1810 from cmu-delphi/ndefries/backfill/on-off-switch
krivard Mar 27, 2023
58b9595
Merge branch 'ndefries/backfill/speed2' into ndefries/backfill/parall…
nmdefries Mar 27, 2023
bf3cd22
Merge pull request #1808 from cmu-delphi/ndefries/backfill/parallel-m…
krivard Mar 27, 2023
7567309
Merge pull request #1812 from cmu-delphi/ndefries/backfill/lp-solver-opt
krivard Mar 27, 2023
0792e19
Merge pull request #1814 from cmu-delphi/ndefries/backfill/speed2
krivard Mar 27, 2023
87d5288
Merge pull request #1800 from cmu-delphi/fix_runner
krivard Mar 29, 2023
70a2988
chore: bump delphi_utils to 0.3.11
Mar 29, 2023
3bb3784
chore: bump covidcast-indicators to 0.3.34
Mar 29, 2023
9fff4ee
[create-pull-request] automated change
krivard Mar 29, 2023
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2 changes: 1 addition & 1 deletion .bumpversion.cfg
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
[bumpversion]
current_version = 0.3.33
current_version = 0.3.34
commit = True
message = chore: bump covidcast-indicators to {new_version}
tag = False
2 changes: 1 addition & 1 deletion .github/workflows/python-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ jobs:
if: github.event.pull_request.draft == false
strategy:
matrix:
packages: [_delphi_utils_python, changehc, claims_hosp, doctor_visits, dsew_community_profile, google_symptoms, hhs_hosp, hhs_facilities, jhu, nchs_mortality, nowcast, quidel_covidtest, safegraph_patterns, sir_complainsalot]
packages: [_delphi_utils_python, changehc, claims_hosp, doctor_visits, dsew_community_profile, google_symptoms, hhs_hosp, jhu, nchs_mortality, nowcast, quidel_covidtest, sir_complainsalot]
defaults:
run:
working-directory: ${{ matrix.packages }}
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2 changes: 1 addition & 1 deletion Jenkinsfile
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
- TODO: #527 Get this list automatically from python-ci.yml at runtime.
*/

def indicator_list = ["backfill_corrections", "changehc", "claims_hosp", "google_symptoms", "hhs_hosp", "jhu", "nchs_mortality", "quidel_covidtest", "safegraph_patterns", "sir_complainsalot", "dsew_community_profile", "doctor_visits"]
def indicator_list = ["backfill_corrections", "changehc", "claims_hosp", "google_symptoms", "hhs_hosp", "jhu", "nchs_mortality", "quidel_covidtest", "sir_complainsalot", "dsew_community_profile", "doctor_visits"]
def build_package_main = [:]
def build_package_prod = [:]
def deploy_staging = [:]
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2 changes: 1 addition & 1 deletion _delphi_utils_python/.bumpversion.cfg
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
[bumpversion]
current_version = 0.3.10
current_version = 0.3.11
commit = True
message = chore: bump delphi_utils to {new_version}
tag = False
Expand Down
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