build: don't install InstaNovo from wheel

pyproject.toml

@@ -6,8 +6,5 @@ readme = "README.md"
 requires-python = ">=3.12"
 dependencies = [
     "gradio>=5.23.1",
-    "instanovo",
+    "instanovo>=1.0.0",
 ]
-
-[tool.uv.sources]
-instanovo = { path = "../dtu-denovo-sequencing/dist/instanovo-1.1.0-py3-none-any.whl" }

requirements.txt

@@ -1,7 +1,5 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --format requirements-txt
-../dtu-denovo-sequencing/dist/instanovo-1.1.0-py3-none-any.whl \
-    --hash=sha256:388ad39f7d458e790e44a9b5655312664e74cee468ce7268fb52740063af557b
 absl-py==2.2.0 \
     --hash=sha256:2aabeae1403380e338fba88d4f8c9bf9925c20ad04c1c96d4a26930d034c507b \
     --hash=sha256:5c432cdf7b045f89c4ddc3bba196cabb389c0c321322f8dec68eecdfa732fdad
@@ -338,6 +336,9 @@ idna==3.10 \
 importlib-resources==6.5.2 \
     --hash=sha256:185f87adef5bcc288449d98fb4fba07cea78bc036455dd44c5fc4a2fe78fed2c \
     --hash=sha256:789cfdc3ed28c78b67a06acb8126751ced69a3d5f79c095a98298cd8a760ccec
+instanovo==1.0.0 \
+    --hash=sha256:f0a1193c2f576cd4f89d3623a7f0bcb42e1031caad2ca2b3b51a8a7a66eb4b41 \
+    --hash=sha256:fd9cfc377d9f8da5272f96b2eb4c14c08b579d7a65466aa402601ec6c4b42672
 isoduration==20.11.0 \
     --hash=sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9 \
     --hash=sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042
@@ -416,9 +417,6 @@ kiwisolver==1.4.8 \
 lark==1.2.2 \
     --hash=sha256:c2276486b02f0f1b90be155f2c8ba4a8e194d42775786db622faccd652d8e80c \
     --hash=sha256:ca807d0162cd16cef15a8feecb862d7319e7a09bdb13aef927968e45040fed80
-lightning==2.5.1 \
-    --hash=sha256:512cbf9e80859f331b329536b2e2f90776e6f8a399048745bb4dabacc36e2850 \
-    --hash=sha256:aca88f8abf3fc38d8b40c1f82ce481f4379c2b181a6eeeb9217db0aba8e40736
 lightning-utilities==0.14.2 \
     --hash=sha256:0466a4f1bb9dff1c7190d4c7a32d1a8a1109f94fb816931efe8fb8b12bb0ab8d \
     --hash=sha256:da791fcaa731f651ec76a1a3b12994ed05af4d6841f2e78760233552709ef05d
@@ -441,7 +439,7 @@ lxml==4.9.4 \
 markdown==3.7 \
     --hash=sha256:2ae2471477cfd02dbbf038d5d9bc226d40def84b4fe2986e49b59b6b472bbed2 \
     --hash=sha256:7eb6df5690b81a1d7942992c97fad2938e956e79df20cbc6186e9c3a77b1c803
-markdown-it-py==3.0.0 \
+markdown-it-py==3.0.0 ; sys_platform != 'emscripten' \
     --hash=sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1 \
     --hash=sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb
 markupsafe==3.0.2 \
@@ -499,7 +497,7 @@ matplotlib==3.10.1 \
     --hash=sha256:dc6ab14a7ab3b4d813b88ba957fc05c79493a037f54e246162033591e770de6f \
     --hash=sha256:e8d2d0e3881b129268585bf4765ad3ee73a4591d77b9a18c214ac7e3a79fb2ba \
     --hash=sha256:e9b4bb156abb8fa5e5b2b460196f7db7264fc6d62678c03457979e7d5254b7be
-mdurl==0.1.2 \
+mdurl==0.1.2 ; sys_platform != 'emscripten' \
     --hash=sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8 \
     --hash=sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba
 monotonic==1.6 \
@@ -870,12 +868,17 @@ pydantic-core==2.27.2 \
 pydub==0.25.1 \
     --hash=sha256:65617e33033874b59d87db603aa1ed450633288aefead953b30bded59cb599a6 \
     --hash=sha256:980a33ce9949cab2a569606b65674d748ecbca4f0796887fd6f46173a7b0d30f
-pygments==2.19.1 \
+pygments==2.19.1 ; sys_platform != 'emscripten' \
     --hash=sha256:61c16d2a8576dc0649d9f39e089b5f02bcd27fba10d8fb4dcc28173f7a45151f \
     --hash=sha256:9ea1544ad55cecf4b8242fab6dd35a93bbce657034b0611ee383099054ab6d8c
 pyjwt==2.10.1 \
     --hash=sha256:3cc5772eb20009233caf06e9d8a0577824723b44e6648ee0a2aedb6cf9381953 \
     --hash=sha256:dcdd193e30abefd5debf142f9adfcdd2b58004e644f25406ffaebd50bd98dacb
+pyopenms==3.3.0 \
+    --hash=sha256:582b585691c0fcfe8ac519849b01c5be861f66059b3c6a6c830cc14d15f20c98 \
+    --hash=sha256:c3774b759975064d764239f2e1dbb59810a66124667bb39451e0602d13120fc7 \
+    --hash=sha256:da7284294fa850b45c206b9337d39c3f9d01b9bfa013665ec0dc55da9513e49c \
+    --hash=sha256:ff05ae5be93235a8f1eebef02c7e27bfc215c30b80f8c4b27d5a159ffe8f5f22
 pyparsing==3.2.3 \
     --hash=sha256:a749938e02d6fd0b59b356ca504a24982314bb090c383e3cf201c95ef7e2bfcf \
     --hash=sha256:b9c13f1ab8b3b542f72e28f634bad4de758ab3ce4546e4301970ad6fa77c38be
@@ -976,7 +979,7 @@ rfc3339-validator==0.1.4 \
 rfc3986-validator==0.1.1 \
     --hash=sha256:2f235c432ef459970b4306369336b9d5dbdda31b510ca1e327636e01f528bfa9 \
     --hash=sha256:3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055
-rich==13.9.4 \
+rich==13.9.4 ; sys_platform != 'emscripten' \
     --hash=sha256:439594978a49a09530cff7ebc4b5c7103ef57baf48d5ea3184f21d9a2befa098 \
     --hash=sha256:6049d5e6ec054bf2779ab3358186963bac2ea89175919d699e378b99738c2a90
 rpds-py==0.23.1 \
@@ -1099,7 +1102,7 @@ semantic-version==2.10.0 \
 setuptools==78.1.0 \
     --hash=sha256:18fd474d4a82a5f83dac888df697af65afa82dec7323d09c3e37d1f14288da54 \
     --hash=sha256:3e386e96793c8702ae83d17b853fb93d3e09ef82ec62722e61da5cd22376dcd8
-shellingham==1.5.4 \
+shellingham==1.5.4 ; sys_platform != 'emscripten' \
     --hash=sha256:7ecfff8f2fd72616f7481040475a65b2bf8af90a56c89140852d1120324e8686 \
     --hash=sha256:8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de
 simplejson==3.20.1 \
@@ -1182,13 +1185,10 @@ torchmetrics==1.7.0 \
 tqdm==4.67.1 \
     --hash=sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2 \
     --hash=sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2
-transfusion-asr==0.1.0 \
-    --hash=sha256:ba7cb988feeb1670335f42e8accc2ca77a1508cbd5cfa5e86eabe35d7be0f3d2 \
-    --hash=sha256:f9026f5450da4ef14be246dc208deefdb857da525092ab182e48c0b8d0a583c5
 triton==3.2.0 ; platform_machine == 'x86_64' and sys_platform == 'linux' \
     --hash=sha256:8d9b215efc1c26fa7eefb9a157915c92d52e000d2bf83e5f69704047e63f125c \
     --hash=sha256:e5dfa23ba84541d7c0a531dfce76d8bcd19159d50a4a8b14ad01e91734a5c1b0
-typer==0.15.2 \
+typer==0.15.2 ; sys_platform != 'emscripten' \
     --hash=sha256:46a499c6107d645a9c13f7ee46c5d5096cae6f5fc57dd11eccbbb9ae3e44ddfc \
     --hash=sha256:ab2fab47533a813c49fe1f16b1a370fd5819099c00b119e0633df65f22144ba5
 types-python-dateutil==2.9.0.20241206 \

uv.lock

@@ -801,67 +801,35 @@ wheels = [
 
 [[package]]
 name = "instanovo"
-version = "1.1.0"
-source = { path = "../dtu-denovo-sequencing/dist/instanovo-1.1.0-py3-none-any.whl" }
+version = "1.0.0"
+source = { registry = "https://pypi.org/simple" }
 dependencies = [
+    { name = "click" },
     { name = "datasets" },
-    { name = "gitpython" },
     { name = "hydra-core" },
     { name = "jaxtyping" },
     { name = "jiwer" },
-    { name = "lightning" },
     { name = "matchms" },
     { name = "neptune" },
     { name = "numpy" },
     { name = "omegaconf" },
     { name = "pandas" },
     { name = "polars" },
-    { name = "pyteomics" },
+    { name = "pyopenms" },
     { name = "python-dotenv" },
-    { name = "pyyaml" },
-    { name = "requests" },
+    { name = "pytorch-lightning" },
     { name = "s3fs" },
     { name = "scikit-learn" },
     { name = "spectrum-utils" },
     { name = "tensorboard" },
+    { name = "torch" },
     { name = "tqdm" },
-    { name = "transfusion-asr" },
-    { name = "typer" },
 ]
+sdist = { url = "https://files.pythonhosted.org/packages/12/a5/e97bec7c26bdd165f23108cb6c048ff50e75c3eced8b08b052c5e0d7ac25/instanovo-1.0.0.tar.gz", hash = "sha256:fd9cfc377d9f8da5272f96b2eb4c14c08b579d7a65466aa402601ec6c4b42672", size = 70720 }
 wheels = [
-    { filename = "instanovo-1.1.0-py3-none-any.whl", hash = "sha256:388ad39f7d458e790e44a9b5655312664e74cee468ce7268fb52740063af557b" },
+    { url = "https://files.pythonhosted.org/packages/10/f2/0f121a26c0b35fa9f962a68864afc75925295b909271e2ad18f2089831a6/instanovo-1.0.0-py3-none-any.whl", hash = "sha256:f0a1193c2f576cd4f89d3623a7f0bcb42e1031caad2ca2b3b51a8a7a66eb4b41", size = 79386 },
 ]
 
-[package.metadata]
-requires-dist = [
-    { name = "datasets", specifier = ">=3.1.0" },
-    { name = "gitpython", specifier = ">=3.1.44" },
-    { name = "hydra-core", specifier = ">=1.3.2" },
-    { name = "jaxtyping", specifier = ">=0.2.34" },
-    { name = "jiwer", specifier = ">=3.0.5" },
-    { name = "lightning", specifier = ">=2.5.1" },
-    { name = "matchms", specifier = ">=0.28.1" },
-    { name = "neptune", specifier = ">=1.13.0" },
-    { name = "numpy", specifier = ">=2.0.2" },
-    { name = "omegaconf", specifier = ">=2.3.0" },
-    { name = "pandas", specifier = ">=2.2.3" },
-    { name = "polars", specifier = ">=1.12.0" },
-    { name = "pyteomics", specifier = ">=4.7.5" },
-    { name = "python-dotenv", specifier = ">=1.0.1" },
-    { name = "pyyaml", specifier = ">=6.0.2" },
-    { name = "requests", specifier = ">=2.32.3" },
-    { name = "s3fs", specifier = ">=2024.9.0" },
-    { name = "scikit-learn", specifier = ">=1.5.2" },
-    { name = "spectrum-utils", specifier = ">=0.4.2" },
-    { name = "tensorboard", specifier = ">=2.18.0" },
-    { name = "torch", marker = "extra == 'cpu'", specifier = ">=2.4.1,<2.5" },
-    { name = "torch", marker = "extra == 'cu124'", specifier = ">=2.4.1,<2.5" },
-    { name = "tqdm", specifier = ">=4.67.0" },
-    { name = "transfusion-asr", specifier = ">=0.1.0" },
-    { name = "typer", specifier = ">=0.15.1" },
-]
-provides-extras = ["cpu", "cu124"]
-
 [[package]]
 name = "instanovo-gradio"
 version = "0.1.0"
@@ -874,7 +842,7 @@ dependencies = [
 [package.metadata]
 requires-dist = [
     { name = "gradio", specifier = ">=5.23.1" },
-    { name = "instanovo", path = "../dtu-denovo-sequencing/dist/instanovo-1.1.0-py3-none-any.whl" },
+    { name = "instanovo", specifier = ">=1.0.0" },
 ]
 
 [[package]]
@@ -1061,26 +1029,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/2d/00/d90b10b962b4277f5e64a78b6609968859ff86889f5b898c1a778c06ec00/lark-1.2.2-py3-none-any.whl", hash = "sha256:c2276486b02f0f1b90be155f2c8ba4a8e194d42775786db622faccd652d8e80c", size = 111036 },
 ]
 
-[[package]]
-name = "lightning"
-version = "2.5.1"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "fsspec", extra = ["http"] },
-    { name = "lightning-utilities" },
-    { name = "packaging" },
-    { name = "pytorch-lightning" },
-    { name = "pyyaml" },
-    { name = "torch" },
-    { name = "torchmetrics" },
-    { name = "tqdm" },
-    { name = "typing-extensions" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/39/53/21a834e03317d04cc3db7307d4c19af94c0db43b9001e8fabb8d150c5e69/lightning-2.5.1.tar.gz", hash = "sha256:aca88f8abf3fc38d8b40c1f82ce481f4379c2b181a6eeeb9217db0aba8e40736", size = 630918 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/80/eb/45f6629b92cb4ed38854d5b76f9f668ff58404a4b9ec1abefa98502afd98/lightning-2.5.1-py3-none-any.whl", hash = "sha256:512cbf9e80859f331b329536b2e2f90776e6f8a399048745bb4dabacc36e2850", size = 818892 },
-]
-
 [[package]]
 name = "lightning-utilities"
 version = "0.14.2"
@@ -1928,6 +1876,22 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/61/ad/689f02752eeec26aed679477e80e632ef1b682313be70793d798c1d5fc8f/PyJWT-2.10.1-py3-none-any.whl", hash = "sha256:dcdd193e30abefd5debf142f9adfcdd2b58004e644f25406ffaebd50bd98dacb", size = 22997 },
 ]
 
+[[package]]
+name = "pyopenms"
+version = "3.3.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "matplotlib" },
+    { name = "numpy" },
+    { name = "pandas" },
+]
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/f5/df/ae6655221fa6b53850cbacae9f6a1d03ee67dba855f8ecb1c5faa01dfec9/pyopenms-3.3.0-cp312-cp312-macosx_13_0_x86_64.whl", hash = "sha256:da7284294fa850b45c206b9337d39c3f9d01b9bfa013665ec0dc55da9513e49c", size = 56065326 },
+    { url = "https://files.pythonhosted.org/packages/14/a1/f0685bd47e00a9ea27056335b94516d4d8451ac5151fb05c0d10fcc3c627/pyopenms-3.3.0-cp312-cp312-macosx_14_0_arm64.whl", hash = "sha256:c3774b759975064d764239f2e1dbb59810a66124667bb39451e0602d13120fc7", size = 50494234 },
+    { url = "https://files.pythonhosted.org/packages/43/40/9c5dc2af36707a7f853b1142af4992e8e9050e1926397a25ec7ba36521ce/pyopenms-3.3.0-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:582b585691c0fcfe8ac519849b01c5be861f66059b3c6a6c830cc14d15f20c98", size = 57231043 },
+    { url = "https://files.pythonhosted.org/packages/d6/5b/363202bb04962d5aa7ea48a8856692eeebe692e578d481e1ad9de7f476cc/pyopenms-3.3.0-cp312-cp312-win_amd64.whl", hash = "sha256:ff05ae5be93235a8f1eebef02c7e27bfc215c30b80f8c4b27d5a159ffe8f5f22", size = 29539839 },
+]
+
 [[package]]
 name = "pyparsing"
 version = "3.2.3"
@@ -2615,15 +2579,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/d0/30/dc54f88dd4a2b5dc8a0279bdd7270e735851848b762aeb1c1184ed1f6b14/tqdm-4.67.1-py3-none-any.whl", hash = "sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2", size = 78540 },
 ]
 
-[[package]]
-name = "transfusion-asr"
-version = "0.1.0"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/0c/61/8b241f67846260f6d24e2f6c10f5a380cc7ede4f0e7619280e18215367c6/transfusion-asr-0.1.0.tar.gz", hash = "sha256:f9026f5450da4ef14be246dc208deefdb857da525092ab182e48c0b8d0a583c5", size = 52935 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/b8/59/c64b155873375427662a6fbdec13833100e79d1c48ac1c258f5e7e922b51/transfusion_asr-0.1.0-py3-none-any.whl", hash = "sha256:ba7cb988feeb1670335f42e8accc2ca77a1508cbd5cfa5e86eabe35d7be0f3d2", size = 54713 },
-]
-
 [[package]]
 name = "triton"
 version = "3.2.0"