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v0.6.0 Release #92

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Dec 22, 2023
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5b6f59c
Add get_records to pipestat_manager and add related test #75
donaldcampbelljr Sep 20, 2023
1544fda
clean up signatures #72
donaldcampbelljr Sep 20, 2023
4523ddc
clean up docstrings
donaldcampbelljr Sep 20, 2023
8d838cc
remove superfluous get_table_name function
donaldcampbelljr Sep 20, 2023
175dc57
Reduce get_orm and get_model into one function. #71
donaldcampbelljr Sep 21, 2023
5220129
Fix CLI to use record-identifier instead of sample-name
donaldcampbelljr Sep 21, 2023
9b6aae1
Fix CLI to use pipeline_type #37
donaldcampbelljr Sep 21, 2023
1722b0f
modify get_records to return new structure https://github.com/pepkit/…
donaldcampbelljr Sep 27, 2023
f02678f
fix html report generation using get_records
donaldcampbelljr Sep 27, 2023
7de7b5e
Merge pull request #83 from pepkit/dev_get_records
donaldcampbelljr Sep 27, 2023
0f90ce7
add simple CLI test for reporting and retrieving #81
donaldcampbelljr Sep 29, 2023
eb64b59
Merge remote-tracking branch 'origin/dev' into dev
donaldcampbelljr Sep 29, 2023
f275e21
Pipestat reader (#80)
donaldcampbelljr Oct 2, 2023
fd96c79
list to List
donaldcampbelljr Oct 2, 2023
99b1380
fixed typing in python3.8
khoroshevskyi Oct 2, 2023
c581afd
update changelog
donaldcampbelljr Oct 2, 2023
b4a316c
fix table_name_bug
donaldcampbelljr Oct 3, 2023
7e63d90
"0.5.4a1" for alpha release
donaldcampbelljr Oct 3, 2023
239d110
"0.6.0a1" for alpha release
donaldcampbelljr Oct 3, 2023
5588510
Dev json schema (#87)
donaldcampbelljr Oct 4, 2023
89119fb
add retrieve_distinct function for #70 and https://github.com/databio…
donaldcampbelljr Oct 6, 2023
2e5dd1c
add `pipestat link` functionality to create symlinks (#90)
donaldcampbelljr Oct 12, 2023
2d89b32
update changelog
donaldcampbelljr Oct 12, 2023
2040c72
clean up docstrings, remove unused variables, refactor link_dir
donaldcampbelljr Oct 12, 2023
9e43274
clean up more docstrings
donaldcampbelljr Oct 12, 2023
a2af669
remove unnecessary print statement to reduce verbosity
donaldcampbelljr Oct 13, 2023
56941ef
Begin work on adding created and modified datetime, DateTime objects …
donaldcampbelljr Oct 13, 2023
040dccd
fix datetime objects #93
donaldcampbelljr Oct 13, 2023
72523d8
fix pipeline_name field beginning with underscore https://github.com/…
donaldcampbelljr Oct 16, 2023
84dafa3
timestamp continuation, list_recent_results does NOT work
donaldcampbelljr Oct 16, 2023
7d124bc
Merge pull request #98 from pepkit/dev_time_stamp
donaldcampbelljr Oct 16, 2023
4be4a9e
fix doc string for schema
donaldcampbelljr Oct 16, 2023
f228c0b
Merge remote-tracking branch 'origin/dev' into dev
donaldcampbelljr Oct 16, 2023
e627ac6
add filtering by created and modified time #93
donaldcampbelljr Oct 16, 2023
622742b
update version for alpha release v0.6.0a2
donaldcampbelljr Oct 17, 2023
01f3c98
fix list reversing #93
donaldcampbelljr Oct 17, 2023
498650c
polish tests #93
donaldcampbelljr Oct 17, 2023
d5baf70
add filebackend list_recent_results, remove records broken #93
donaldcampbelljr Oct 17, 2023
362c745
fix remove records bug #93
donaldcampbelljr Oct 17, 2023
cbbb3f7
update doc strings #93
donaldcampbelljr Oct 17, 2023
7638088
Merge pull request #100 from pepkit/dev_time_stamp
donaldcampbelljr Oct 17, 2023
359117d
update change log for list_recent_results
donaldcampbelljr Oct 17, 2023
cd1295d
begin work on retrieve_multiple #96
donaldcampbelljr Oct 17, 2023
448dfc2
add db backend, test broken #96
donaldcampbelljr Oct 17, 2023
8f51452
fix db backend logic #96
donaldcampbelljr Oct 18, 2023
5a163b3
implement file backend #96
donaldcampbelljr Oct 18, 2023
fb02932
fix docstrings
donaldcampbelljr Oct 19, 2023
35a96e0
some minor polishing
donaldcampbelljr Oct 19, 2023
032e434
update readme
donaldcampbelljr Oct 19, 2023
c6bd122
move pipestat reader per #22
donaldcampbelljr Oct 19, 2023
47073da
fix pipestat reader setup and manifest per #22
donaldcampbelljr Oct 19, 2023
af9d1a5
Add optional dependencies via setup #22
donaldcampbelljr Oct 19, 2023
5ce2d93
pipestat can now run without DB specific dependencies #22
donaldcampbelljr Oct 19, 2023
ac310a2
Some refactoring #64
donaldcampbelljr Oct 20, 2023
9a79135
add other requirements to test
donaldcampbelljr Oct 20, 2023
b8173b9
refactor to have ParsedSchemaDB inherit from ParsedSchema for code re…
donaldcampbelljr Oct 20, 2023
5b74b19
Clean up
donaldcampbelljr Oct 20, 2023
1b7ce00
return total record count #75
donaldcampbelljr Oct 20, 2023
92f593f
make initialization of file and DB backend into separate functions
donaldcampbelljr Oct 24, 2023
a9c8ed2
add decorator for checking dependencies
donaldcampbelljr Oct 24, 2023
b2fb9fa
polishing decorator for checking dependencies
donaldcampbelljr Oct 25, 2023
0a3a85b
consolidate decorator and ancillary function into one
donaldcampbelljr Oct 25, 2023
9dcfb3b
Merge pull request #101 from pepkit/dev_retrieve_multiple
donaldcampbelljr Oct 25, 2023
c45b046
Merge branch 'dev' of github.com:pepkit/pipestat into dev_move_reader…
donaldcampbelljr Oct 25, 2023
96038a1
Merge pull request #102 from pepkit/dev_move_reader_dependencies
donaldcampbelljr Oct 25, 2023
debcecd
first pass #99, some tests broken
donaldcampbelljr Oct 25, 2023
12545ea
fix all tests #99
donaldcampbelljr Oct 26, 2023
c1e8b2b
refactor store to cfg #99
donaldcampbelljr Oct 26, 2023
8c19cb2
fix bug with table path
donaldcampbelljr Oct 26, 2023
df4eed8
setitem is now a wrapper for report
donaldcampbelljr Oct 26, 2023
4b96cc9
fix getitem implementation, add test #99
donaldcampbelljr Oct 26, 2023
18ef632
Begin work on select_records, retrieve_one, retrieve_many #103
donaldcampbelljr Oct 26, 2023
a73a30a
Implement select_records, and cursor pagination #103
donaldcampbelljr Oct 26, 2023
8aba8ba
clarify init message
nsheff Oct 27, 2023
6301b86
Update dbbackend.py
nsheff Oct 27, 2023
c5cb162
add loading JSON and column.contains for filtering #103
donaldcampbelljr Oct 27, 2023
df7eacd
testing differences
donaldcampbelljr Oct 27, 2023
2fc3bfb
add or_ and and_ sqlmodel operators #103
donaldcampbelljr Oct 27, 2023
e5888c1
some comments
donaldcampbelljr Oct 27, 2023
c0b4178
steps toward smarter pytesting
nsheff Oct 27, 2023
616def4
#103 -- added multi key filter
khoroshevskyi Oct 27, 2023
fc74052
Merge branch 'dev' of github.com:pepkit/pipestat into pytests
nsheff Oct 27, 2023
7cdb2d2
typo
nsheff Oct 27, 2023
795d3c2
polish changes to select_records and add tests. #103
donaldcampbelljr Oct 30, 2023
40783c6
Merge remote-tracking branch 'origin/dev' into dev_99_103_API_Refactor
donaldcampbelljr Oct 30, 2023
c89178e
fix typo
donaldcampbelljr Oct 30, 2023
78fe1f1
remove Union for python 3.8 compat
donaldcampbelljr Oct 30, 2023
231063e
move get_nested_column and define_sqlalchemy_type outside of select_r…
donaldcampbelljr Oct 30, 2023
dc465b7
update doc strings
donaldcampbelljr Oct 30, 2023
b71d387
Modify to be true JSONs chema with using $ref and $def for custom obj…
donaldcampbelljr Oct 30, 2023
3864f87
Update pipestat/backends/abstract.py
donaldcampbelljr Oct 30, 2023
e6d50c1
Update pipestat/backends/db_backend/dbbackend.py
donaldcampbelljr Oct 30, 2023
a04e84d
Update pipestat/backends/db_backend/dbbackend.py
donaldcampbelljr Oct 30, 2023
539836f
Update pipestat/pipestat.py
donaldcampbelljr Oct 30, 2023
d9e4e32
Update pipestat/pipestat.py
donaldcampbelljr Oct 30, 2023
ad2d8e9
Update tests/data/sample_output_schema.yaml
donaldcampbelljr Oct 30, 2023
e03335d
Polish PR, fix docstrings, add wrapper for remove
donaldcampbelljr Oct 30, 2023
7a5f1f5
remove unnecessary mutablemapping inheritance
donaldcampbelljr Oct 30, 2023
a98213a
lint
donaldcampbelljr Oct 30, 2023
96ef53f
cleaning
khoroshevskyi Oct 31, 2023
b38f6bd
fixed failing test
khoroshevskyi Oct 31, 2023
e03da51
remove old, unused validate_schema function
donaldcampbelljr Oct 31, 2023
52fe125
change ALL output_schemas to reflect JSON schema
donaldcampbelljr Oct 31, 2023
92786e0
lint
donaldcampbelljr Oct 31, 2023
a1d79bb
per request, remove select function as well as dynamic_filter
donaldcampbelljr Oct 31, 2023
3816b33
add to do
donaldcampbelljr Oct 31, 2023
b4f2591
revert PipestatManager to a MutableMapping
donaldcampbelljr Oct 31, 2023
d8c257c
remove select_txt and select_distinct
donaldcampbelljr Oct 31, 2023
eef4ae7
revert select_distinct for now
donaldcampbelljr Oct 31, 2023
c84e510
remove unused backend funcs, tests broken
donaldcampbelljr Oct 31, 2023
55947b9
implement list_recent_results wrapper (DBBackend only)
donaldcampbelljr Oct 31, 2023
cba1625
implement list_recent_results wrapper (DBBackend only)
donaldcampbelljr Oct 31, 2023
9e1345c
some polish, begin implementing select_records
donaldcampbelljr Oct 31, 2023
ca2118c
more work towards select_records
donaldcampbelljr Oct 31, 2023
eb652e6
change operator func, add list comprehension for sets
donaldcampbelljr Nov 1, 2023
c07e9d6
implement AND OR Logic and fix tests, add sorting
donaldcampbelljr Nov 1, 2023
c3d3fb0
fix time stamp filtering if NOT nested
donaldcampbelljr Nov 1, 2023
779e2b3
lint and fix db test
donaldcampbelljr Nov 1, 2023
a7a5ba0
attempt to pare down results based on columns, does not work.
donaldcampbelljr Nov 1, 2023
6aa12fa
add column filtering for filebackend, add tests, add no filter condit…
donaldcampbelljr Nov 2, 2023
98d9dc8
fix complex object filtering
donaldcampbelljr Nov 2, 2023
191b1ed
implement select_distinct for filebackend
donaldcampbelljr Nov 2, 2023
5c8c361
select_dsitinct now works on record identifiers for filebackend, poli…
donaldcampbelljr Nov 2, 2023
29f30da
fix retrieve_one and retrieve_many for filebackend
donaldcampbelljr Nov 2, 2023
eeba387
fix timestamp test for filebackend
donaldcampbelljr Nov 2, 2023
f104c7f
use isinstance for type checking
donaldcampbelljr Nov 2, 2023
d39115a
Merge branch 'dev' of github.com:pepkit/pipestat into dev
nsheff Nov 3, 2023
6985fcd
Merge pull request #109 from pepkit/dev_modify_JSON_Schema
donaldcampbelljr Nov 3, 2023
a2e7da6
refactored for efficiency
khoroshevskyi Nov 3, 2023
dcea34d
Merge branch 'dev' into dev_99_103_API_Refactor
donaldcampbelljr Nov 3, 2023
4204b6c
fix recursive schema after merge
donaldcampbelljr Nov 3, 2023
97d1952
remove get_records, fix return type for select_records if given columns
donaldcampbelljr Nov 3, 2023
8742864
begin remove of get_one_record
donaldcampbelljr Nov 3, 2023
407b37a
deleted get_one_record function
khoroshevskyi Nov 3, 2023
da46b55
fix get_status on dbbackend using select_records
donaldcampbelljr Nov 3, 2023
01dcc4f
remove retrieve from dbbackend and reports
donaldcampbelljr Nov 3, 2023
2b1e275
replace retrieve with retrieve_one and begin replacing retrieve with …
donaldcampbelljr Nov 3, 2023
4bd9254
lint
donaldcampbelljr Nov 3, 2023
558e59b
fix select_records filebackend bug, remove retrieve from tests
donaldcampbelljr Nov 4, 2023
29b372b
finish removing retrieve function
donaldcampbelljr Nov 4, 2023
82bf36e
attempt re-implementing record not found error for retrieve_one and r…
donaldcampbelljr Nov 4, 2023
18a72e8
fix bugs with select_records and RecordNotFound, implement ColumnNotF…
donaldcampbelljr Nov 6, 2023
6e1938b
Merge pull request #108 from pepkit/dev_99_103_API_Refactor
donaldcampbelljr Nov 6, 2023
7f4af4f
merge changes from dev
donaldcampbelljr Nov 6, 2023
19998d0
lint
donaldcampbelljr Nov 6, 2023
b4041db
update changelog and version for 0.6.0a3 release
donaldcampbelljr Nov 6, 2023
3ee7ac2
refactoring based on ruff
khoroshevskyi Nov 6, 2023
79cd9eb
update cli and usage and api docs, lint
donaldcampbelljr Nov 6, 2023
c6f3d5b
update documentation focused on schemas
donaldcampbelljr Nov 6, 2023
0603d58
add result_identifier as parameter to retrieve_one
donaldcampbelljr Nov 6, 2023
67e42d3
add result_identifier as parameter to retrieve_many
donaldcampbelljr Nov 6, 2023
52272dd
__version__ = "0.6.0a4"
donaldcampbelljr Nov 6, 2023
84cbf88
Finish adding pytest.mark.skipif
donaldcampbelljr Nov 7, 2023
b13c88e
Merge branch 'dev' into pytests
donaldcampbelljr Nov 7, 2023
74d4fd3
lint
donaldcampbelljr Nov 7, 2023
08fa3e9
Merge pull request #107 from pepkit/pytests
donaldcampbelljr Nov 7, 2023
a6e1e66
move general tests to test_pipestat, remove some redundancy
donaldcampbelljr Nov 7, 2023
4d1d268
implement clear_status pytest for filebackend #110
donaldcampbelljr Nov 7, 2023
619d8bd
polish test set_item, report_overwrite
donaldcampbelljr Nov 7, 2023
4e497c4
add pytest fixture val_dict
donaldcampbelljr Nov 7, 2023
c3a8527
Merge branch 'dev' of github.com:pepkit/pipestat into dev
nsheff Nov 7, 2023
dfd2ddc
add pytest fixture values_sample, values_project
donaldcampbelljr Nov 7, 2023
bf994c8
add pytest fixture values_complex_linking, move fixtures to conftest.py
donaldcampbelljr Nov 7, 2023
d42b47a
deleted unnecessary print
khoroshevskyi Nov 7, 2023
6a95af1
add test_select_no_filter_limit
donaldcampbelljr Nov 7, 2023
60bd1bf
black formatting
khoroshevskyi Nov 7, 2023
f955fd9
add pytest fixture for ranges
donaldcampbelljr Nov 7, 2023
8e2c5c3
Merge pull request #112 from pepkit/pytests
donaldcampbelljr Nov 7, 2023
3c7d8f5
lint
donaldcampbelljr Nov 7, 2023
6ba6c36
fix record_identifier being returned twice if it is an input column
donaldcampbelljr Nov 7, 2023
423115d
fix typo
nsheff Nov 7, 2023
1a1932a
change retrieve_one output to no longer we wrapped by select_records …
donaldcampbelljr Nov 7, 2023
f9b467e
Merge remote-tracking branch 'origin/dev' into dev
donaldcampbelljr Nov 7, 2023
8fccf1a
fix schema propert to return psm.cfg["_schema"].to_dict()
donaldcampbelljr Nov 7, 2023
f10d462
fix schema propert to return psm.cfg["_schema"]
donaldcampbelljr Nov 7, 2023
a36accc
add psm.schema.original_schema to parsed schema
donaldcampbelljr Nov 7, 2023
65ae9d4
add r_id = record_identifier or self.record_identifier to retrieve_one
donaldcampbelljr Nov 7, 2023
4b14d5c
fix majority of tests due to retrieve_one
donaldcampbelljr Nov 7, 2023
ec59cfe
lint
donaldcampbelljr Nov 7, 2023
3136b3a
fix table creation bug with retrieve_one
donaldcampbelljr Nov 7, 2023
3e093de
remove RecordNotFoundError because it breaks pypiper
donaldcampbelljr Nov 7, 2023
2eec3d5
fix parsed_schema json schema parsing to be correct hierarchy
donaldcampbelljr Nov 7, 2023
ae9e9f4
update jupyter api docs
donaldcampbelljr Nov 7, 2023
4a3e439
update cli docs
donaldcampbelljr Nov 7, 2023
428f117
fix property access #113
donaldcampbelljr Nov 7, 2023
687845b
add retrieving multiple results using retrieve_one
donaldcampbelljr Nov 8, 2023
50abdf1
list to List
donaldcampbelljr Nov 8, 2023
0aa53a1
add quickstart guide
donaldcampbelljr Nov 8, 2023
50db365
add psm.schema.resolved_schema
donaldcampbelljr Nov 8, 2023
48ad7fa
remove unused function
donaldcampbelljr Nov 8, 2023
f0c4bb8
version bump to v0.6.0a5
donaldcampbelljr Nov 8, 2023
830ba1a
fix config_path property
donaldcampbelljr Nov 8, 2023
363a54c
re-implement RecordNotFoundError
donaldcampbelljr Nov 8, 2023
ef50dff
be more selective about which exceptions to pass
nsheff Nov 9, 2023
d119e9f
potential solution for #117
donaldcampbelljr Nov 9, 2023
5bdfb51
Merge remote-tracking branch 'origin/dev' into dev
donaldcampbelljr Nov 9, 2023
e979b41
version bump 0.6.0a6
donaldcampbelljr Nov 9, 2023
766e4a1
remove redundant pydantic
donaldcampbelljr Nov 9, 2023
f226c9f
fix pipestat reader dependency checking
donaldcampbelljr Nov 9, 2023
11613b7
fix cli bug regarding env variables
donaldcampbelljr Nov 9, 2023
6e9f465
retrieve_one record_identifier defaults to None to allow for use with…
donaldcampbelljr Nov 9, 2023
db68369
further documentation polishing
donaldcampbelljr Nov 9, 2023
efa6eaf
fix obtaining record_identifier from cfg file
donaldcampbelljr Nov 9, 2023
d69e4e9
correct config.md
donaldcampbelljr Nov 9, 2023
6f1ecbc
correct pipestat_specification.md
donaldcampbelljr Nov 9, 2023
12de0ec
Merge branch 'master' into dev
donaldcampbelljr Nov 9, 2023
b414330
0.6.0a7 prerelease
donaldcampbelljr Nov 15, 2023
dfa7616
Clarify return on select_records
donaldcampbelljr Nov 16, 2023
b8795da
ensure requirements list yacman>= 0.9.2
donaldcampbelljr Nov 16, 2023
275cd26
potential fix for #119
donaldcampbelljr Nov 17, 2023
b916c81
change warning to debug for creating status table
donaldcampbelljr Nov 20, 2023
76d79d9
fix pipestat creating subdirectories before creating results file.
donaldcampbelljr Nov 27, 2023
6bc5230
First proof of concept for #120
donaldcampbelljr Nov 28, 2023
1b31357
simply do replacement at beginning
donaldcampbelljr Nov 28, 2023
29992b4
Fixed #106
khoroshevskyi Nov 28, 2023
a923e4b
Merge pull request #121 from pepkit/105_new_sqlmodel
khoroshevskyi Nov 28, 2023
a202dd6
now functional, create aggregate_results.yaml which replaces self._da…
donaldcampbelljr Nov 29, 2023
887ed07
replace spaces in names with %20 during html link generation
donaldcampbelljr Nov 29, 2023
5712a60
fix reported_objs bug
donaldcampbelljr Nov 29, 2023
03d7d1a
expandpath for link_dir during pipestat link
donaldcampbelljr Nov 29, 2023
17563fd
add tests for new aggregate_results functionality
donaldcampbelljr Nov 30, 2023
e52adc2
Merge pull request #123 from pepkit/dev_multi_results
donaldcampbelljr Nov 30, 2023
81ca9f2
refactor db-backend to dbbackend
donaldcampbelljr Dec 5, 2023
1f5412b
fix stats and objects buttons for summary page #130
donaldcampbelljr Dec 8, 2023
c855ce2
fix stats table on summary page #130
donaldcampbelljr Dec 8, 2023
aa12e1e
fix broken status if multi_results_files #130
donaldcampbelljr Dec 8, 2023
e9836a8
fix log and profile files #130
donaldcampbelljr Dec 8, 2023
d28d19b
fix tsv columns #130
donaldcampbelljr Dec 8, 2023
9e8140d
Add check for pipeline type during report generation #130
donaldcampbelljr Dec 11, 2023
9d34da7
refactor Sample to Record #130
donaldcampbelljr Dec 11, 2023
91cde59
fix refactor for sample page
donaldcampbelljr Dec 11, 2023
3daba6f
fix stats.tsv and objects.yaml generation to incorporate pipeline types
donaldcampbelljr Dec 11, 2023
f015074
add project_objects page #130
donaldcampbelljr Dec 11, 2023
9e57162
minor polishing
donaldcampbelljr Dec 11, 2023
43ef21d
remove temp test
donaldcampbelljr Dec 11, 2023
a31f7f1
lint
donaldcampbelljr Dec 11, 2023
ffc9bf5
add passing looper's samples to pipestat summarize to populate table
donaldcampbelljr Dec 11, 2023
3db1040
remove unused code
donaldcampbelljr Dec 14, 2023
7a37128
Merge pull request #131 from pepkit/dev_fix_reporting
donaldcampbelljr Dec 14, 2023
53a1c37
version bump for pre-release v0.6.0a9
donaldcampbelljr Dec 14, 2023
c784a95
use "object_type" for image and file types or fall back on using "typ…
donaldcampbelljr Dec 15, 2023
2bbe665
ensure project level objects are accurate on summary/index page
donaldcampbelljr Dec 18, 2023
9f3ee8e
remove project name from stats and object file names
donaldcampbelljr Dec 18, 2023
6cf6f58
update changelog
donaldcampbelljr Dec 18, 2023
23808cd
0.6.0a10 bump for pre-release
donaldcampbelljr Dec 18, 2023
8241748
allow project-level figures to display as columns instead of rows
donaldcampbelljr Dec 20, 2023
7dc0711
0.6.0a11 pre-release
donaldcampbelljr Dec 20, 2023
ede50e3
v0.6.0 release prep
donaldcampbelljr Dec 22, 2023
cd2a5ee
Merge branch 'master' into dev
donaldcampbelljr Dec 22, 2023
b53976f
lint
donaldcampbelljr Dec 22, 2023
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5 changes: 5 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -137,3 +137,8 @@ dmypy.json
# Pyre type checker
.pyre/
/tests/data/reports/
/tests/data/test_default_pipeline_name_objs_summary.yaml
/tests/data/test_default_pipeline_name_stats_summary.tsv
/tests/data/test_file_links/link_results/
/tests/data/default_pipeline_name_objs_summary.yaml
/tests/data/default_pipeline_name_stats_summary.tsv
3 changes: 3 additions & 0 deletions MANIFEST.in
Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,7 @@ include requirements/*
include README.md
include pipestat/schemas/*
include pipestat/backends/*
include pipestat/backends/file_backend/*
include pipestat/backends/db_backend/*
include pipestat/pipestatreader/*
include pipestat/jinja_templates/*
1 change: 0 additions & 1 deletion README.md
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Expand Up @@ -18,7 +18,6 @@ First you need a local demo instance of posgres running to test the database bac

```
docker run --rm -it -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pipestat-password -e POSTGRES_DB=pipestat-test -p 5432:5432 postgres

```

Then, run tests:
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8 changes: 4 additions & 4 deletions docs/README.md
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Expand Up @@ -25,9 +25,8 @@ pip install pipestat

```console
export PIPESTAT_RESULTS_SCHEMA=output_schema.yaml
export PIPESTAT_SAMPLE_NAME=my_record
export PIPESTAT_RECORD_IDENTIFIER=my_record
export PIPESTAT_RESULTS_FILE=results_file.yaml
export PIPESTAT_PROJECT_NAME=my_namespace
```
Note: When setting environment variables as in the above example, you will need to provide an output_schema.yaml file in your current working directory with the following example data:
```
Expand All @@ -37,6 +36,7 @@ result_name:
```

## Pipeline results reporting and retrieval
### For these examples below, it is assumed that the proper environment variables (see above) have been set.

### Report a result

Expand All @@ -60,7 +60,7 @@ psm.report(values={"result_name": 1.1})
From command line:

```console
pipestat retrieve -i result_name
pipestat retrieve -r my_record
```

From Python:
Expand All @@ -69,7 +69,7 @@ From Python:
import pipestat

psm = pipestat.PipestatManager()
psm.retrieve(result_identifier="result_name")
psm.retrieve_one(result_identifier="result_name")
```

## Pipeline status management
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