explicite requirement txt for stable and loose

MannLabs · Sep 12, 2024 · 38dd362 · 38dd362
1 parent d275dd4
commit 38dd362
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Showing 10 changed files with 92 additions and 15 deletions.
diff --git a/peptdeep/__init__.py b/peptdeep/__init__.py
@@ -50,6 +50,10 @@
     "PyPi": __pypi__,
 }
 __extra_requirements__ = {
-    "development": "requirements_development.txt",
-    "gui": "requirements_gui.txt",
+    "development-stable": "development-stable.txt",
+    "gui-stable": "gui-stable.txt",
+    "hla-stable": "hla-stable.txt",
+    "development": "development.txt",
+    "gui": "gui.txt",
+    "hla": "hla.txt",
 }
diff --git a/requirements/requirements.txt → requirements/base-stable.txt b/requirements/requirements.txt → requirements/base-stable.txt
diff --git a/requirements/base.txt b/requirements/base.txt
@@ -0,0 +1,20 @@
+pywin32; sys_platform=='win32'
+pythonnet; sys_platform=='win32'
+
+click
+pandas
+numpy<2
+torch
+tqdm
+numba
+psutil
+biopython
+transformers
+scikit-learn
+streamlit-aggrid
+lxml
+pyteomics
+
+streamlit>=1.23.0
+alphabase>=1.1.0
+alpharaw>=0.2.0
diff --git a/requirements/requirements_development.txt → requirements/development-stable.txt b/requirements/requirements_development.txt → requirements/development-stable.txt
diff --git a/requirements/development.txt b/requirements/development.txt
@@ -0,0 +1,44 @@
+pywin32; sys_platform=='win32'
+pythonnet; sys_platform=='win32'
+
+jupyter
+twine
+bumpversion
+pipdeptree
+ipykernel
+tqdm
+wget
+pyinstaller
+
+click
+pandas
+numpy<2
+seaborn
+matplotlib
+numba
+psutil
+biopython
+streamlit-aggrid # df interact
+transformers
+scikit-learn
+lxml
+
+# sphinx
+autodocsumm
+myst_parser
+sphinx
+nbsphinx
+jinja2
+contextfilter
+furo
+
+#--extra-index-url https://download.pytorch.org/whl/cu116
+torch
+
+streamlit>=1.23.0
+alphabase>=1.1.0
+alpharaw>=0.2.0
+
+pytest
+pre-commit==3.7.0
+nbmake==1.5.3
diff --git a/requirements/requirements_gui.txt → requirements/gui-stable.txt b/requirements/requirements_gui.txt → requirements/gui-stable.txt
diff --git a/requirements/gui.txt b/requirements/gui.txt
@@ -0,0 +1,19 @@
+pywin32; sys_platform=='win32'
+pythonnet; sys_platform=='win32'
+
+click
+pandas
+numpy<2
+torch
+tqdm
+numba
+psutil
+biopython
+transformers
+scikit-learn
+streamlit-aggrid
+lxml
+
+streamlit>=1.23.0
+alphabase>=1.1.0
+alpharaw>=0.2.0
diff --git a/requirements/requirements_hla.txt → requirements/hla-stable.txt b/requirements/requirements_hla.txt → requirements/hla-stable.txt
diff --git a/requirements/hla.txt b/requirements/hla.txt
@@ -0,0 +1 @@
+pydivsufsort # used by alphabase.protein.lcp_digest
diff --git a/setup.py b/setup.py
@@ -18,27 +18,16 @@ def get_long_description():
 def get_requirements():
     extra_requirements = {}
     requirement_file_names = package2install.__extra_requirements__
-    requirement_file_names[""] = "requirements.txt"
+    requirement_file_names[""] = "base.txt"
     for extra, requirement_file_name in requirement_file_names.items():
         full_requirement_file_name = os.path.join(
             "requirements",
             requirement_file_name,
         )
         with open(full_requirement_file_name) as requirements_file:
-            if extra != "":
-                extra_stable = f"{extra}-stable"
-            else:
-                extra_stable = "stable"
-            extra_requirements[extra_stable] = []
             extra_requirements[extra] = []
             for line in requirements_file:
-                extra_requirements[extra_stable].append(line)
-                # conditional requirements like: pywin32; sys_platform=='win32'
-                line, *conditions = line.split(";")
-                requirement, *comparison = re.split("[><=~!]", line)
-                requirement = requirement.strip()
-                requirement = ";".join([requirement] + conditions)
-                extra_requirements[extra].append(requirement)
+                extra_requirements[extra].append(line)
     requirements = extra_requirements.pop("")
     return requirements, extra_requirements