diff --git a/core/README.md b/core/README.md
index 8eda8be0..cc0380f6 100644
--- a/core/README.md
+++ b/core/README.md
@@ -1,5 +1,5 @@
 # eolearn.core subpackage
 
-The main subpackage which implements basic building blocks (EOPatch, EOTask and EOWorkflow) and commonly used functionalities.
+The deprecated way to install `eolearn.core`. See [migration guide](https://github.com/sentinel-hub/eo-learn/issues/733) on how to correctly install the `eo-learn` package.
 
-For more information about the module visit [readthedocs](https://eo-learn.readthedocs.io/en/latest/reference/eolearn.core.html), or see the [module task index](https://eo-learn.readthedocs.io/en/latest/eotasks.html#core).
+Installs requirements and a dummy package that is detected by `eo-learn` but otherwise does not change anything.
diff --git a/core/deprecated_eolearn_core/__init__.py b/core/deprecated_eolearn_core/__init__.py
new file mode 100644
index 00000000..5b601886
--- /dev/null
+++ b/core/deprecated_eolearn_core/__init__.py
@@ -0,0 +1 @@
+__version__ = "1.5.0"
diff --git a/core/setup.py b/core/setup.py
index d431fc03..00a8026d 100644
--- a/core/setup.py
+++ b/core/setup.py
@@ -18,7 +18,7 @@ def parse_requirements(file):
 
 
 def get_version():
-    path = os.path.join(os.path.dirname(__file__), "eolearn", "core", "__init__.py")
+    path = os.path.join(os.path.dirname(__file__), "deprecated_eolearn_core", "__init__.py")
     with open(path) as version_file:
         for line in version_file:
             if line.find("__version__") >= 0:
@@ -44,15 +44,12 @@ def get_version():
     author="Sinergise EO research team",
     author_email="eoresearch@sinergise.com",
     license="MIT",
-    packages=find_packages(exclude=["eolearn.tests*"]),
-    package_data={"eolearn": ["core/py.typed"]},
-    include_package_data=True,
+    packages=find_packages(),
     install_requires=parse_requirements("requirements.txt"),
     extras_require={
         "RAY": parse_requirements("requirements-ray.txt"),
         "ZARR": parse_requirements("requirements-zarr.txt"),
     },
-    zip_safe=False,
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",
diff --git a/coregistration/README.md b/coregistration/README.md
index 407a914b..94fdede8 100644
--- a/coregistration/README.md
+++ b/coregistration/README.md
@@ -1,5 +1,5 @@
 # eolearn.coregistration subpackage
 
-A collection of tools and EOTasks for image co-registration
+The deprecated way to install `eolearn.coregistration`. See [migration guide](https://github.com/sentinel-hub/eo-learn/issues/733) on how to correctly install the `eo-learn` package.
 
-For more information about the module visit [readthedocs](https://eo-learn.readthedocs.io/en/latest/reference/eolearn.coregistration.html), or see the [module task index](https://eo-learn.readthedocs.io/en/latest/eotasks.html#coregistration).
+Installs requirements and a dummy package that is detected by `eo-learn` but otherwise does not change anything.
diff --git a/coregistration/deprecated_eolearn_coregistration/__init__.py b/coregistration/deprecated_eolearn_coregistration/__init__.py
new file mode 100644
index 00000000..5b601886
--- /dev/null
+++ b/coregistration/deprecated_eolearn_coregistration/__init__.py
@@ -0,0 +1 @@
+__version__ = "1.5.0"
diff --git a/coregistration/requirements.txt b/coregistration/requirements.txt
index 0b5b46e2..150d5c82 100644
--- a/coregistration/requirements.txt
+++ b/coregistration/requirements.txt
@@ -1,3 +1,2 @@
 # using headless version of opencv, otherwise gitlab runners fail
-eo-learn-core
 opencv-python-headless
diff --git a/coregistration/setup.py b/coregistration/setup.py
index fd76eb52..e09b78e5 100644
--- a/coregistration/setup.py
+++ b/coregistration/setup.py
@@ -18,7 +18,7 @@ def parse_requirements(file):
 
 
 def get_version():
-    path = os.path.join(os.path.dirname(__file__), "eolearn", "coregistration", "__init__.py")
+    path = os.path.join(os.path.dirname(__file__), "deprecated_eolearn_coregistration", "__init__.py")
     with open(path) as version_file:
         for line in version_file:
             if line.find("__version__") >= 0:
@@ -45,9 +45,7 @@ def get_version():
     author_email="eoresearch@sinergise.com",
     license="MIT",
     packages=find_packages(),
-    include_package_data=True,
     install_requires=parse_requirements("requirements.txt"),
-    zip_safe=False,
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",
diff --git a/eolearn/__init__.py b/eolearn/__init__.py
index 0f4393e5..c3566b29 100644
--- a/eolearn/__init__.py
+++ b/eolearn/__init__.py
@@ -1,2 +1,16 @@
 """Main module of the `eolearn` package."""
 __version__ = "1.4.2"
+
+import importlib.util
+import warnings
+
+SUBPACKAGES = ["core", "coregistration", "features", "geometry", "io", "mask", "ml_tools", "visualization"]
+deprecated_installs = [
+    subpackage for subpackage in SUBPACKAGES if importlib.util.find_spec(f"deprecated_eolearn_{subpackage}") is not None
+]
+if deprecated_installs:
+    warnings.warn(
+        f"You are currently using an outdated installation of `eo-learn` for submodules {deprecated_installs}. You can"
+        " find instructions on how to install `eo-learn` correctly at"
+        " https://github.com/sentinel-hub/eo-learn/issues/733."
+    )
diff --git a/features/README.md b/features/README.md
index e477f5a9..15664d2c 100644
--- a/features/README.md
+++ b/features/README.md
@@ -1,5 +1,5 @@
 # eolearn.features subpackage
 
-A collection of utilities for extracting data properties and feature manipulation.
+The deprecated way to install `eolearn.features`. See [migration guide](https://github.com/sentinel-hub/eo-learn/issues/733) on how to correctly install the `eo-learn` package.
 
-For more information about the module visit [readthedocs](https://eo-learn.readthedocs.io/en/latest/reference/eolearn.features.html), or see the [module task index](https://eo-learn.readthedocs.io/en/latest/eotasks.html#features).
+Installs requirements and a dummy package that is detected by `eo-learn` but otherwise does not change anything.
diff --git a/features/deprecated_eolearn_features/__init__.py b/features/deprecated_eolearn_features/__init__.py
new file mode 100644
index 00000000..5b601886
--- /dev/null
+++ b/features/deprecated_eolearn_features/__init__.py
@@ -0,0 +1 @@
+__version__ = "1.5.0"
diff --git a/features/requirements.txt b/features/requirements.txt
index 1e4813f6..3ea2d507 100644
--- a/features/requirements.txt
+++ b/features/requirements.txt
@@ -1,4 +1,3 @@
-eo-learn-core
 numba>=0.53.0
 numpy
 pillow>=9.1.0
diff --git a/features/setup.py b/features/setup.py
index d5902903..d1e869c8 100644
--- a/features/setup.py
+++ b/features/setup.py
@@ -18,7 +18,7 @@ def parse_requirements(file):
 
 
 def get_version():
-    path = os.path.join(os.path.dirname(__file__), "eolearn", "features", "__init__.py")
+    path = os.path.join(os.path.dirname(__file__), "deprecated_eolearn_features", "__init__.py")
     with open(path) as version_file:
         for line in version_file:
             if line.find("__version__") >= 0:
@@ -45,9 +45,7 @@ def get_version():
     author_email="eoresearch@sinergise.com",
     license="MIT",
     packages=find_packages(),
-    include_package_data=True,
     install_requires=parse_requirements("requirements.txt"),
-    zip_safe=False,
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",
diff --git a/geometry/README.md b/geometry/README.md
index eed6ec3c..7dbf06e4 100644
--- a/geometry/README.md
+++ b/geometry/README.md
@@ -1,5 +1,5 @@
 # eolearn.geometry subpackage
 
-Geometry subpackage used for geometric transformation and conversion between vector and raster data.
+The deprecated way to install `eolearn.geometry`. See [migration guide](https://github.com/sentinel-hub/eo-learn/issues/733) on how to correctly install the `eo-learn` package.
 
-For more information about the module visit [readthedocs](https://eo-learn.readthedocs.io/en/latest/reference/eolearn.geometry.html), or see the [module task index](https://eo-learn.readthedocs.io/en/latest/eotasks.html#geometry).
+Installs requirements and a dummy package that is detected by `eo-learn` but otherwise does not change anything.
diff --git a/geometry/deprecated_eolearn_geometry/__init__.py b/geometry/deprecated_eolearn_geometry/__init__.py
new file mode 100644
index 00000000..5b601886
--- /dev/null
+++ b/geometry/deprecated_eolearn_geometry/__init__.py
@@ -0,0 +1 @@
+__version__ = "1.5.0"
diff --git a/geometry/requirements.txt b/geometry/requirements.txt
index 9218ee7f..44d262fa 100644
--- a/geometry/requirements.txt
+++ b/geometry/requirements.txt
@@ -1,4 +1,3 @@
-eo-learn-core
 geopandas>=0.8.1
 rasterio>=1.2.7, <1.3.8
 scikit-image>=0.15.0
diff --git a/geometry/setup.py b/geometry/setup.py
index 476057df..5a4ead37 100644
--- a/geometry/setup.py
+++ b/geometry/setup.py
@@ -18,7 +18,7 @@ def parse_requirements(file):
 
 
 def get_version():
-    path = os.path.join(os.path.dirname(__file__), "eolearn", "geometry", "__init__.py")
+    path = os.path.join(os.path.dirname(__file__), "deprecated_eolearn_geometry", "__init__.py")
     with open(path) as version_file:
         for line in version_file:
             if line.find("__version__") >= 0:
@@ -45,9 +45,7 @@ def get_version():
     author_email="eoresearch@sinergise.com",
     license="MIT",
     packages=find_packages(),
-    include_package_data=True,
     install_requires=parse_requirements("requirements.txt"),
-    zip_safe=False,
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",
diff --git a/io/README.md b/io/README.md
index 24784741..c989e1bb 100644
--- a/io/README.md
+++ b/io/README.md
@@ -1,5 +1,5 @@
 # eolearn.io subpackage
 
-Input/output subpackage that deals with obtaining data from Sentinel Hub services or saving and loading data locally.
+The deprecated way to install `eolearn.io`. See [migration guide](https://github.com/sentinel-hub/eo-learn/issues/733) on how to correctly install the `eo-learn` package.
 
-For more information about the module visit [readthedocs](https://eo-learn.readthedocs.io/en/latest/reference/eolearn.io.html), or see the [module task index](https://eo-learn.readthedocs.io/en/latest/eotasks.html#io).
+Installs requirements and a dummy package that is detected by `eo-learn` but otherwise does not change anything.
diff --git a/io/deprecated_eolearn_io/__init__.py b/io/deprecated_eolearn_io/__init__.py
new file mode 100644
index 00000000..5b601886
--- /dev/null
+++ b/io/deprecated_eolearn_io/__init__.py
@@ -0,0 +1 @@
+__version__ = "1.5.0"
diff --git a/io/requirements.txt b/io/requirements.txt
index 6bc455e5..0b16c413 100644
--- a/io/requirements.txt
+++ b/io/requirements.txt
@@ -1,6 +1,5 @@
 affine
 boto3
-eo-learn-core
 fiona>=1.8.18
 geopandas>=0.8.1
 rasterio>=1.2.7, <1.3.8
diff --git a/io/setup.py b/io/setup.py
index aa4891ce..6bdea282 100644
--- a/io/setup.py
+++ b/io/setup.py
@@ -18,7 +18,7 @@ def parse_requirements(file):
 
 
 def get_version():
-    path = os.path.join(os.path.dirname(__file__), "eolearn", "io", "__init__.py")
+    path = os.path.join(os.path.dirname(__file__), "deprecated_eolearn_io", "__init__.py")
     with open(path) as version_file:
         for line in version_file:
             if line.find("__version__") >= 0:
@@ -45,10 +45,8 @@ def get_version():
     author_email="eoresearch@sinergise.com",
     license="MIT",
     packages=find_packages(),
-    include_package_data=True,
     install_requires=parse_requirements("requirements.txt"),
     extras_require={"METEOBLUE": parse_requirements("requirements-meteoblue.txt")},
-    zip_safe=False,
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",
diff --git a/mask/README.md b/mask/README.md
index 8229d08e..bcb6f7ff 100644
--- a/mask/README.md
+++ b/mask/README.md
@@ -1,5 +1,5 @@
 # eolearn.mask subpackage
 
-The subpackage is used for masking of data and calculation of cloud masks.
+The deprecated way to install `eolearn.mask`. See [migration guide](https://github.com/sentinel-hub/eo-learn/issues/733) on how to correctly install the `eo-learn` package.
 
-For more information about the module visit [readthedocs](https://eo-learn.readthedocs.io/en/latest/reference/eolearn.mask.html), or see the [module task index](https://eo-learn.readthedocs.io/en/latest/eotasks.html#mask).
+Installs requirements and a dummy package that is detected by `eo-learn` but otherwise does not change anything.
diff --git a/mask/deprecated_eolearn_mask/__init__.py b/mask/deprecated_eolearn_mask/__init__.py
new file mode 100644
index 00000000..5b601886
--- /dev/null
+++ b/mask/deprecated_eolearn_mask/__init__.py
@@ -0,0 +1 @@
+__version__ = "1.5.0"
diff --git a/mask/requirements.txt b/mask/requirements.txt
index 2f17dd18..1a3a5467 100644
--- a/mask/requirements.txt
+++ b/mask/requirements.txt
@@ -1,5 +1,4 @@
 # using headless version of opencv, otherwise gitlab runners fail
-eo-learn-core
 lightgbm>=2.0.11, <4
 numpy
 opencv-python-headless
diff --git a/mask/setup.py b/mask/setup.py
index 5d78748e..8d7e1ce6 100644
--- a/mask/setup.py
+++ b/mask/setup.py
@@ -18,7 +18,7 @@ def parse_requirements(file):
 
 
 def get_version():
-    path = os.path.join(os.path.dirname(__file__), "eolearn", "mask", "__init__.py")
+    path = os.path.join(os.path.dirname(__file__), "deprecated_eolearn_mask", "__init__.py")
     with open(path) as version_file:
         for line in version_file:
             if line.find("__version__") >= 0:
@@ -45,15 +45,7 @@ def get_version():
     author_email="eoresearch@sinergise.com",
     license="MIT",
     packages=find_packages(),
-    include_package_data=True,
-    package_data={
-        "eolearn.mask": [
-            "models/pixel_s2_cloud_detector_lightGBM_v0.2.txt",
-            "models/ssim_s2_cloud_detector_lightGBM_v0.2.txt",
-        ]
-    },
     install_requires=parse_requirements("requirements.txt"),
-    zip_safe=False,
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",
diff --git a/ml_tools/MANIFEST.in b/ml_tools/MANIFEST.in
deleted file mode 100644
index 970f8603..00000000
--- a/ml_tools/MANIFEST.in
+++ /dev/null
@@ -1,5 +0,0 @@
-include requirements*.txt
-include LICENSE
-include README.md
-include eolearn/ml_tools/py.typed
-exclude eolearn/tests/*
diff --git a/ml_tools/README.md b/ml_tools/README.md
index e0b5d137..148a28ee 100644
--- a/ml_tools/README.md
+++ b/ml_tools/README.md
@@ -1,5 +1,5 @@
 # eolearn.ml_tools subpackage
 
-Various tools that can be used before or after the machine learning process.
+The deprecated way to install `eolearn.ml_tools`. See [migration guide](https://github.com/sentinel-hub/eo-learn/issues/733) on how to correctly install the `eo-learn` package.
 
-For more information about the module visit [readthedocs](https://eo-learn.readthedocs.io/en/latest/reference/eolearn.ml-tools.html), or see the [module task index](https://eo-learn.readthedocs.io/en/latest/eotasks.html#ml-tools).
+Installs requirements and a dummy package that is detected by `eo-learn` but otherwise does not change anything.
diff --git a/ml_tools/deprecated_eolearn_ml_tools/__init__.py b/ml_tools/deprecated_eolearn_ml_tools/__init__.py
new file mode 100644
index 00000000..5b601886
--- /dev/null
+++ b/ml_tools/deprecated_eolearn_ml_tools/__init__.py
@@ -0,0 +1 @@
+__version__ = "1.5.0"
diff --git a/ml_tools/requirements.txt b/ml_tools/requirements.txt
index c9775b16..21a9abe7 100644
--- a/ml_tools/requirements.txt
+++ b/ml_tools/requirements.txt
@@ -1,3 +1,2 @@
-eo-learn-core
 numpy
 shapely
diff --git a/ml_tools/setup.py b/ml_tools/setup.py
index eb910d86..26a21315 100644
--- a/ml_tools/setup.py
+++ b/ml_tools/setup.py
@@ -18,7 +18,7 @@ def parse_requirements(file):
 
 
 def get_version():
-    path = os.path.join(os.path.dirname(__file__), "eolearn", "ml_tools", "__init__.py")
+    path = os.path.join(os.path.dirname(__file__), "deprecated_eolearn_ml_tools", "__init__.py")
     with open(path) as version_file:
         for line in version_file:
             if line.find("__version__") >= 0:
@@ -45,13 +45,11 @@ def get_version():
     author_email="eoresearch@sinergise.com",
     license="MIT",
     packages=find_packages(),
-    include_package_data=True,
     install_requires=parse_requirements("requirements.txt"),
     extras_require={
         "PLOTTING": parse_requirements("requirements-plotting.txt"),
         "TDIGEST": parse_requirements("requirements-tdigest.txt"),
     },
-    zip_safe=False,
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",
diff --git a/visualization/README.md b/visualization/README.md
index f8aa261f..3f562974 100644
--- a/visualization/README.md
+++ b/visualization/README.md
@@ -1,5 +1,5 @@
 # eolearn.visualization subpackage
 
-A collection of data visualization utilities.
+The deprecated way to install `eolearn.visualization`. See [migration guide](https://github.com/sentinel-hub/eo-learn/issues/733) on how to correctly install the `eo-learn` package.
 
-For more information about the module visit [readthedocs](https://eo-learn.readthedocs.io/en/latest/reference/eolearn.visualization.html).
+Installs requirements and a dummy package that is detected by `eo-learn` but otherwise does not change anything.
diff --git a/visualization/deprecated_eolearn_visualization/__init__.py b/visualization/deprecated_eolearn_visualization/__init__.py
new file mode 100644
index 00000000..5b601886
--- /dev/null
+++ b/visualization/deprecated_eolearn_visualization/__init__.py
@@ -0,0 +1 @@
+__version__ = "1.5.0"
diff --git a/visualization/requirements.txt b/visualization/requirements.txt
index 8cfba60e..17cff14c 100644
--- a/visualization/requirements.txt
+++ b/visualization/requirements.txt
@@ -1,4 +1,3 @@
-eo-learn-core
 graphviz>=0.10.1
 jinja2
 matplotlib
diff --git a/visualization/setup.py b/visualization/setup.py
index bec11d81..8201d00a 100644
--- a/visualization/setup.py
+++ b/visualization/setup.py
@@ -18,7 +18,7 @@ def parse_requirements(file):
 
 
 def get_version():
-    path = os.path.join(os.path.dirname(__file__), "eolearn", "visualization", "__init__.py")
+    path = os.path.join(os.path.dirname(__file__), "deprecated_eolearn_visualization", "__init__.py")
     with open(path) as version_file:
         for line in version_file:
             if line.find("__version__") >= 0:
@@ -46,9 +46,7 @@ def get_version():
     license="MIT",
     packages=find_packages(),
     package_data={"eolearn": ["visualization/report_templates/report.html"]},
-    include_package_data=True,
     install_requires=parse_requirements("requirements.txt"),
-    zip_safe=False,
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",