I finally solved the issue. The cause is two-fold:

The correct conda library path is $HOME/miniconda/envs/some_env/lib because I created a virtual env named some_env for everything. So, I needed to add export LD_LIBRARY_PATH="$HOME/miniconda/envs/some_env/lib:$LD_LIBRARY_PATH.
cudatoolkit was in fact installed as pytorch’s dependency, but the version was wrong. Installing only pytorch 0.3.0 will install cudatoolkit 9.0 as dependency, while pytorch itself is compiled with cudatoolkit 8.0 (as indicated by the build string py36_cuda8.0.61_cudnn7.0.3h37a80b5_4). So, I needed to explicitly specify cudatoolkit version: conda install -y -c pytorch pytorch=0.3.0 cudatoolkit=8.0


The complete .travis.yml file is:
language: python
before_install:
  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
  - bash ~/miniconda.sh -b -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  - conda update -y conda
  - conda create -y -n some_env python=3.6
  - source activate some_env
  - conda install -y -c pytorch pytorch=0.3.0 cudatoolkit=8.0  # specify cudatoolkit version explicitly
  - export LD_LIBRARY_PATH="$HOME/miniconda/envs/some_env/lib:$LD_LIBRARY_PATH"  # add conda library path
install:
  - pip install -r requirements.txt
  - pip install .
script: pytest --cov
after_success: coveralls

Now the build succeeds again. Thanks for pointing me to the right direction 
P.S. I find it weird that cudatoolkit 9.0 is installed instead of 8.0 which pytorch 0.3.0 is compiled with. Why is that?