From 1984bec9e692bf79286059dd2f447546e0f51dd2 Mon Sep 17 00:00:00 2001 From: George Thomas Date: Mon, 30 Sep 2024 08:31:16 -0700 Subject: [PATCH 1/5] (PPS-710): replace github reference with PyPI version --- poetry.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4253d8d..4885faa 100644 --- a/poetry.lock +++ b/poetry.lock @@ -892,4 +892,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = ">=3.9,<4" -content-hash = "46f6becbde49e3d4884ba14c2b32e0a48ddcf005df94a655bf13a818a2084bf3" +content-hash = "bfe0a0f52eb8043c34502463f1df7d4b360fb3d88b345c39e08db5d95f0f960b" diff --git a/pyproject.toml b/pyproject.toml index 72bea65..ee8194f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,7 @@ gen3dictionary = "*" pyyaml = "<7" rstr = ">=3,<4" requests = "*" -dictionaryutils = {git = "https://github.com/uc-cdis/dictionaryutils", rev = "3.4.11"} +dictionaryutils = ">=3.4.11" psqlgraph = "*" [tool.poetry.dev-dependencies] From 91ef148056bab71d5c4b2767cb8f1fd49a5f863e Mon Sep 17 00:00:00 2001 From: George Thomas Date: Mon, 30 Sep 2024 10:30:44 -0700 Subject: [PATCH 2/5] (PPS-710): test new branch of gen3datamodel --- poetry.lock | 29 ++++++++++++----------------- pyproject.toml | 3 ++- 2 files changed, 14 insertions(+), 18 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4885faa..50a0120 100644 --- a/poetry.lock +++ b/poetry.lock @@ -257,9 +257,10 @@ name = "dictionaryutils" version = "3.4.11" description = "Python wrapper and metaschema for datadictionary." optional = false -python-versions = ">=3.9, <4" -files = [] -develop = false +python-versions = "<4,>=3.9" +files = [ + {file = "dictionaryutils-3.4.11.tar.gz", hash = "sha256:a63ae34b4c0130cd94e4ca685cbb18155c225f9bface32ed1d503393d0dd39cf"}, +] [package.dependencies] cdislogging = "*" @@ -267,12 +268,6 @@ jsonschema = "<=4.23.0" PyYAML = "*" requests = "*" -[package.source] -type = "git" -url = "https://github.com/uc-cdis/dictionaryutils" -reference = "3.4.11" -resolved_reference = "cbac4bf51febc64eab4875f84ca6cb15c8b4718e" - [[package]] name = "exceptiongroup" version = "1.2.2" @@ -303,12 +298,12 @@ PyYAML = "*" [package.source] type = "git" url = "https://github.com/NCI-GDC/gdcdictionary.git" -reference = "release/py3" -resolved_reference = "b5db4e815794c0544bbc9f4b6a16fc5b0475363b" +reference = "2.0.0" +resolved_reference = "0427dc737a7cc165868f3d065529d20a68a20ac1" [[package]] name = "gen3datamodel" -version = "3.2.0" +version = "3.2.2" description = "" optional = false python-versions = "^3.9" @@ -317,8 +312,8 @@ develop = false [package.dependencies] cdislogging = "*" -dictionaryutils = {git = "https://github.com/uc-cdis/dictionaryutils", rev = "3.4.11"} -gdcdictionary = {git = "https://github.com/NCI-GDC/gdcdictionary.git", rev = "release/py3"} +dictionaryutils = ">=3.4.11" +gdcdictionary = {git = "https://github.com/NCI-GDC/gdcdictionary.git", rev = "2.0.0"} jsonschema = "*" psqlgraph = "~=3.0" psycopg2-binary = "~=2.8.2" @@ -330,8 +325,8 @@ strict-rfc3339 = "==0.7" [package.source] type = "git" url = "https://github.com/uc-cdis/gen3datamodel" -reference = "3.2.1" -resolved_reference = "97d67c7bd2539f9d90ea0ccb899185ebe2ecc24c" +reference = "chore/update-branches" +resolved_reference = "02f70838c66389cfdfd49c662cf1dc561c9c0e7d" [[package]] name = "gen3dictionary" @@ -892,4 +887,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = ">=3.9,<4" -content-hash = "bfe0a0f52eb8043c34502463f1df7d4b360fb3d88b345c39e08db5d95f0f960b" +content-hash = "12600bd8e2754864d03cf92ca9e27b45ff3d5b61b7498c1006e87a51fd3e01cc" diff --git a/pyproject.toml b/pyproject.toml index ee8194f..80495a7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,8 @@ data-simulator = 'datasimulator.main:main' [tool.poetry.dependencies] python = ">=3.9,<4" cdislogging = "*" -gen3datamodel = {git = "https://github.com/uc-cdis/gen3datamodel", rev = "3.2.1"} +# gen3datamodel = {git = "https://github.com/uc-cdis/gen3datamodel", rev = "3.2.1"} +gen3datamodel = {git = "https://github.com/uc-cdis/gen3datamodel", branch = "chore/update-branches"} gen3dictionary = "*" pyyaml = "<7" rstr = ">=3,<4" From 75c332dbf9232d40bb8040cdaca9248cc467e30a Mon Sep 17 00:00:00 2001 From: George Thomas Date: Tue, 1 Oct 2024 07:48:05 -0700 Subject: [PATCH 3/5] (PPS-710): update gen3datamodel to PyPI version 3.2.1 --- poetry.lock | 48 ++++++++++++------------------------------------ pyproject.toml | 5 ++--- 2 files changed, 14 insertions(+), 39 deletions(-) diff --git a/poetry.lock b/poetry.lock index 50a0120..b04d291 100644 --- a/poetry.lock +++ b/poetry.lock @@ -282,51 +282,27 @@ files = [ [package.extras] test = ["pytest (>=6)"] -[[package]] -name = "gdcdictionary" -version = "2.0.0" -description = "" -optional = false -python-versions = "*" -files = [] -develop = true - -[package.dependencies] -jsonschema = "*" -PyYAML = "*" - -[package.source] -type = "git" -url = "https://github.com/NCI-GDC/gdcdictionary.git" -reference = "2.0.0" -resolved_reference = "0427dc737a7cc165868f3d065529d20a68a20ac1" - [[package]] name = "gen3datamodel" -version = "3.2.2" +version = "3.2.3" description = "" optional = false -python-versions = "^3.9" -files = [] -develop = false +python-versions = "<4.0,>=3.9" +files = [ + {file = "gen3datamodel-3.2.3-py3-none-any.whl", hash = "sha256:1d892e399282e8a1d3f471a7905c62f59e9deb57568d20aba15e7d9df276a678"}, + {file = "gen3datamodel-3.2.3.tar.gz", hash = "sha256:df2bda8be42879d0b25df13665aaacee854037b1509b62dc2a21df8e25f07d16"}, +] [package.dependencies] cdislogging = "*" dictionaryutils = ">=3.4.11" -gdcdictionary = {git = "https://github.com/NCI-GDC/gdcdictionary.git", rev = "2.0.0"} jsonschema = "*" -psqlgraph = "~=3.0" -psycopg2-binary = "~=2.8.2" -pyrsistent = "==0.15.4" +psqlgraph = ">=3.0,<4.0" +psycopg2-binary = ">=2.8.2,<2.9.0" +pyrsistent = "0.15.4" pytz = "*" -sqlalchemy = "==1.3.3" -strict-rfc3339 = "==0.7" - -[package.source] -type = "git" -url = "https://github.com/uc-cdis/gen3datamodel" -reference = "chore/update-branches" -resolved_reference = "02f70838c66389cfdfd49c662cf1dc561c9c0e7d" +sqlalchemy = "1.3.3" +strict-rfc3339 = "0.7" [[package]] name = "gen3dictionary" @@ -887,4 +863,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = ">=3.9,<4" -content-hash = "12600bd8e2754864d03cf92ca9e27b45ff3d5b61b7498c1006e87a51fd3e01cc" +content-hash = "6bd4b6ba171328eceb8f5e1e2fe068ffa7061034580caca9796d0cd0007480c6" diff --git a/pyproject.toml b/pyproject.toml index 80495a7..72c1bb5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "data-simulator" -version = "1.6.4" +version = "1.6.5" description = "Gen3 Data Simulator" authors = ["CTDS UChicago "] license = "Apache-2.0" @@ -16,8 +16,7 @@ data-simulator = 'datasimulator.main:main' [tool.poetry.dependencies] python = ">=3.9,<4" cdislogging = "*" -# gen3datamodel = {git = "https://github.com/uc-cdis/gen3datamodel", rev = "3.2.1"} -gen3datamodel = {git = "https://github.com/uc-cdis/gen3datamodel", branch = "chore/update-branches"} +gen3datamodel = ">=3.2.1" gen3dictionary = "*" pyyaml = "<7" rstr = ">=3,<4" From a4f29167af47a84dcc405bb7b554b832945d92d4 Mon Sep 17 00:00:00 2001 From: George Thomas Date: Tue, 1 Oct 2024 08:43:17 -0700 Subject: [PATCH 4/5] (PPS-710): add pypi.yaml --- .github/workflows/pypi.yaml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 .github/workflows/pypi.yaml diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml new file mode 100644 index 0000000..5a45f71 --- /dev/null +++ b/.github/workflows/pypi.yaml @@ -0,0 +1,16 @@ +name: PyPI +on: + push: + tags: + - '*' +jobs: + PyPIPoetryPublish: + name: PyPI Poetry Publish + uses: uc-cdis/.github/.github/workflows/python_package_index_publish.yaml@master + with: + PYTHON_VERSION: '3.9' + # This will attempt push to test PyPI first and only push to prod if it works + DO_TEST_PUBLISH_FIRST: true + secrets: + PYPI_TEST_API_TOKEN: ${{ secrets.PYPI_TEST_API_TOKEN }} + PYPI_PROD_API_TOKEN: ${{ secrets.PYPI_PROD_API_TOKEN }} From 2209f163b0744583ee787b7f1778f2147af9029a Mon Sep 17 00:00:00 2001 From: George Thomas Date: Tue, 1 Oct 2024 09:28:43 -0700 Subject: [PATCH 5/5] (PPS-710): remove pypi.yaml --- .github/workflows/pypi.yaml | 16 ---------------- 1 file changed, 16 deletions(-) delete mode 100644 .github/workflows/pypi.yaml diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml deleted file mode 100644 index 5a45f71..0000000 --- a/.github/workflows/pypi.yaml +++ /dev/null @@ -1,16 +0,0 @@ -name: PyPI -on: - push: - tags: - - '*' -jobs: - PyPIPoetryPublish: - name: PyPI Poetry Publish - uses: uc-cdis/.github/.github/workflows/python_package_index_publish.yaml@master - with: - PYTHON_VERSION: '3.9' - # This will attempt push to test PyPI first and only push to prod if it works - DO_TEST_PUBLISH_FIRST: true - secrets: - PYPI_TEST_API_TOKEN: ${{ secrets.PYPI_TEST_API_TOKEN }} - PYPI_PROD_API_TOKEN: ${{ secrets.PYPI_PROD_API_TOKEN }}