diff --git a/dvc/cache/base.py b/dvc/cache/base.py
index 64617ef994..a6c5596d77 100644
--- a/dvc/cache/base.py
+++ b/dvc/cache/base.py
@@ -276,8 +276,6 @@ def save(self, path_info, tree, hash_info, save_link=True, **kwargs):
                 self.tree.scheme,
             )
 
-        if not hash_info:
-            hash_info = self.tree.save_info(path_info, tree=tree, **kwargs)
         hash_ = hash_info[self.tree.PARAM_CHECKSUM]
         return self._save(path_info, tree, hash_, save_link, **kwargs)
 
diff --git a/dvc/command/check_ignore.py b/dvc/command/check_ignore.py
index c611bdbd34..8840dc57ba 100644
--- a/dvc/command/check_ignore.py
+++ b/dvc/command/check_ignore.py
@@ -70,7 +70,6 @@ def run(self):
             ret = self._interactive_mode()
         else:
             ret = self._normal_mode()
-
         return ret
 
 
diff --git a/dvc/command/remote.py b/dvc/command/remote.py
index db622a378b..1cb4a3a869 100644
--- a/dvc/command/remote.py
+++ b/dvc/command/remote.py
@@ -3,7 +3,7 @@
 
 from dvc.command.base import append_doc_link, fix_subparsers
 from dvc.command.config import CmdConfig
-from dvc.config import ConfigError
+from dvc.config import ConfigError, merge
 from dvc.utils import format_link
 
 logger = logging.getLogger(__name__)
@@ -18,7 +18,7 @@ def __init__(self, args):
 
     def _check_exists(self, conf):
         if self.args.name not in conf["remote"]:
-            raise ConfigError(f"remote '{self.args.name}' doesn't exists.")
+            raise ConfigError(f"remote '{self.args.name}' doesn't exist.")
 
 
 class CmdRemoteAdd(CmdRemote):
@@ -61,7 +61,12 @@ def run(self):
 class CmdRemoteModify(CmdRemote):
     def run(self):
         with self.config.edit(self.args.level) as conf:
-            self._check_exists(conf)
+            merged = self.config.load_config_to_level(self.args.level)
+            merge(merged, conf)
+            self._check_exists(merged)
+
+            if self.args.name not in conf["remote"]:
+                conf["remote"][self.args.name] = {}
             section = conf["remote"][self.args.name]
             if self.args.unset:
                 section.pop(self.args.option, None)
diff --git a/dvc/config.py b/dvc/config.py
index 68cda1bece..26181e4d67 100644
--- a/dvc/config.py
+++ b/dvc/config.py
@@ -400,7 +400,7 @@ def load_config_to_level(self, level=None):
             if merge_level == level:
                 break
             if merge_level in self.files:
-                _merge(merged_conf, self.load_one(merge_level))
+                merge(merged_conf, self.load_one(merge_level))
         return merged_conf
 
     @contextmanager
@@ -414,7 +414,7 @@ def edit(self, level="repo"):
         conf = self._save_paths(conf, self.files[level])
 
         merged_conf = self.load_config_to_level(level)
-        _merge(merged_conf, conf)
+        merge(merged_conf, conf)
         self.validate(merged_conf)
 
         self._save_config(level, conf)
@@ -453,11 +453,11 @@ def _pack_remotes(conf):
     return result
 
 
-def _merge(into, update):
+def merge(into, update):
     """Merges second dict into first recursively"""
     for key, val in update.items():
         if isinstance(into.get(key), dict) and isinstance(val, dict):
-            _merge(into[key], val)
+            merge(into[key], val)
         else:
             into[key] = val
 
diff --git a/dvc/dependency/repo.py b/dvc/dependency/repo.py
index eb3c58b5ce..7dffd2eca5 100644
--- a/dvc/dependency/repo.py
+++ b/dvc/dependency/repo.py
@@ -67,7 +67,7 @@ def _get_checksum(self, locked=True):
                     return self.repo.cache.local.tree.get_hash(path, tree=tree)
                 return tree.get_file_hash(path)
 
-    def status(self):
+    def workspace_status(self):
         current_checksum = self._get_checksum(locked=True)
         updated_checksum = self._get_checksum(locked=False)
 
@@ -76,6 +76,9 @@ def status(self):
 
         return {}
 
+    def status(self):
+        return self.workspace_status()
+
     def save(self):
         pass
 
diff --git a/dvc/external_repo.py b/dvc/external_repo.py
index 15332e7de1..c2de3d8e81 100644
--- a/dvc/external_repo.py
+++ b/dvc/external_repo.py
@@ -90,15 +90,26 @@ def use_cache(self, cache):
         """Use the specified cache in place of default tmpdir cache for
         download operations.
         """
-        if hasattr(self, "cache"):
-            save_cache = self.cache.local
-            self.cache.local = cache
+        has_cache = hasattr(self, "cache")
+
+        if has_cache:
+            save_cache = self.cache.local  # pylint: disable=E0203
+            self.cache.local = cache  # pylint: disable=E0203
+        else:
+            from collections import namedtuple
+
+            mock_cache = namedtuple("MockCache", ["local"])(local=cache)
+            self.cache = mock_cache  # pylint: disable=W0201
+
         self._local_cache = cache
 
         yield
 
-        if hasattr(self, "cache"):
+        if has_cache:
             self.cache.local = save_cache
+        else:
+            del self.cache
+
         self._local_cache = None
 
     @cached_property
@@ -130,14 +141,17 @@ def download_update(result):
         for path in paths:
             if not self.repo_tree.exists(path):
                 raise PathMissingError(path, self.url)
-            save_info = self.local_cache.save(
+            hash_info = self.repo_tree.save_info(
+                path, download_callback=download_update
+            )
+            self.local_cache.save(
                 path,
                 self.repo_tree,
-                None,
+                hash_info,
                 save_link=False,
                 download_callback=download_update,
             )
-            save_infos.append(save_info)
+            save_infos.append(hash_info)
 
         return sum(download_results), failed, save_infos
 
diff --git a/dvc/output/base.py b/dvc/output/base.py
index 242499fc55..f17e3df9e5 100644
--- a/dvc/output/base.py
+++ b/dvc/output/base.py
@@ -199,10 +199,7 @@ def changed_cache(self, filter_info=None):
 
         return self.cache.changed_cache(self.checksum, filter_info=filter_info)
 
-    def status(self):
-        if self.checksum and self.use_cache and self.changed_cache():
-            return {str(self): "not in cache"}
-
+    def workspace_status(self):
         if not self.exists:
             return {str(self): "deleted"}
 
@@ -214,6 +211,12 @@ def status(self):
 
         return {}
 
+    def status(self):
+        if self.checksum and self.use_cache and self.changed_cache():
+            return {str(self): "not in cache"}
+
+        return self.workspace_status()
+
     def changed(self):
         status = self.status()
         logger.debug(str(status))
@@ -280,6 +283,7 @@ def save(self):
         self.info = self.save_info()
 
     def commit(self):
+        assert self.info
         if self.use_cache:
             self.cache.save(self.path_info, self.cache.tree, self.info)
 
diff --git a/dvc/repo/tree.py b/dvc/repo/tree.py
index 2b7810c29d..8011d0318c 100644
--- a/dvc/repo/tree.py
+++ b/dvc/repo/tree.py
@@ -245,6 +245,9 @@ class RepoTree(BaseTree):  # pylint:disable=abstract-method
     Any kwargs will be passed to `DvcTree()`.
     """
 
+    scheme = "local"
+    PARAM_CHECKSUM = "md5"
+
     def __init__(self, repo, **kwargs):
         super().__init__(repo, {"url": repo.root_dir})
         if hasattr(repo, "dvc_dir"):
diff --git a/dvc/stage/__init__.py b/dvc/stage/__init__.py
index 6316793bb5..0048c94fb9 100644
--- a/dvc/stage/__init__.py
+++ b/dvc/stage/__init__.py
@@ -396,7 +396,7 @@ def ignore_outs(self):
 
     @staticmethod
     def _changed_entries(entries):
-        return [str(entry) for entry in entries if entry.changed_checksum()]
+        return [str(entry) for entry in entries if entry.workspace_status()]
 
     def _changed_stage_entry(self):
         return f"'md5' of {self} changed."
diff --git a/dvc/tree/base.py b/dvc/tree/base.py
index 700513b19f..1860bafab6 100644
--- a/dvc/tree/base.py
+++ b/dvc/tree/base.py
@@ -236,22 +236,17 @@ def is_dir_hash(cls, hash_):
             return False
         return hash_.endswith(cls.CHECKSUM_DIR_SUFFIX)
 
-    def get_hash(self, path_info, tree=None, **kwargs):
+    def get_hash(self, path_info, **kwargs):
         assert path_info and (
             isinstance(path_info, str) or path_info.scheme == self.scheme
         )
 
-        if not tree:
-            tree = self
-
-        if not tree.exists(path_info):
+        if not self.exists(path_info):
             return None
 
-        if tree == self:
-            # pylint: disable=assignment-from-none
-            hash_ = self.state.get(path_info)
-        else:
-            hash_ = None
+        # pylint: disable=assignment-from-none
+        hash_ = self.state.get(path_info)
+
         # If we have dir hash in state db, but dir cache file is lost,
         # then we need to recollect the dir via .get_dir_hash() call below,
         # see https://github.com/iterative/dvc/issues/2219 for context
@@ -267,10 +262,10 @@ def get_hash(self, path_info, tree=None, **kwargs):
         if hash_:
             return hash_
 
-        if tree.isdir(path_info):
-            hash_ = self.get_dir_hash(path_info, tree, **kwargs)
+        if self.isdir(path_info):
+            hash_ = self.get_dir_hash(path_info, **kwargs)
         else:
-            hash_ = tree.get_file_hash(path_info)
+            hash_ = self.get_file_hash(path_info)
 
         if hash_ and self.exists(path_info):
             self.state.save(path_info, hash_)
@@ -280,12 +275,12 @@ def get_hash(self, path_info, tree=None, **kwargs):
     def get_file_hash(self, path_info):
         raise NotImplementedError
 
-    def get_dir_hash(self, path_info, tree, **kwargs):
+    def get_dir_hash(self, path_info, **kwargs):
         if not self.cache:
             raise RemoteCacheRequiredError(path_info)
 
-        dir_info = self._collect_dir(path_info, tree, **kwargs)
-        return self._save_dir_info(dir_info, path_info)
+        dir_info = self._collect_dir(path_info, **kwargs)
+        return self._save_dir_info(dir_info)
 
     def hash_to_path_info(self, hash_):
         return self.path_info / hash_[0:2] / hash_[2:]
@@ -298,29 +293,26 @@ def path_to_hash(self, path):
 
         return "".join(parts)
 
-    def save_info(self, path_info, tree=None, **kwargs):
-        return {
-            self.PARAM_CHECKSUM: self.get_hash(path_info, tree=tree, **kwargs)
-        }
+    def save_info(self, path_info, **kwargs):
+        return {self.PARAM_CHECKSUM: self.get_hash(path_info, **kwargs)}
 
-    @staticmethod
-    def _calculate_hashes(file_infos, tree):
+    def _calculate_hashes(self, file_infos):
         file_infos = list(file_infos)
         with Tqdm(
             total=len(file_infos),
             unit="md5",
             desc="Computing file/dir hashes (only done once)",
         ) as pbar:
-            worker = pbar.wrap_fn(tree.get_file_hash)
-            with ThreadPoolExecutor(max_workers=tree.hash_jobs) as executor:
+            worker = pbar.wrap_fn(self.get_file_hash)
+            with ThreadPoolExecutor(max_workers=self.hash_jobs) as executor:
                 tasks = executor.map(worker, file_infos)
                 hashes = dict(zip(file_infos, tasks))
         return hashes
 
-    def _collect_dir(self, path_info, tree, **kwargs):
+    def _collect_dir(self, path_info, **kwargs):
         file_infos = set()
 
-        for fname in tree.walk_files(path_info, **kwargs):
+        for fname in self.walk_files(path_info, **kwargs):
             if DvcIgnore.DVCIGNORE_FILE == fname.name:
                 raise DvcIgnoreInCollectedDirError(fname.parent)
 
@@ -329,7 +321,7 @@ def _collect_dir(self, path_info, tree, **kwargs):
         hashes = {fi: self.state.get(fi) for fi in file_infos}
         not_in_state = {fi for fi, hash_ in hashes.items() if hash_ is None}
 
-        new_hashes = self._calculate_hashes(not_in_state, tree)
+        new_hashes = self._calculate_hashes(not_in_state)
         hashes.update(new_hashes)
 
         result = [
@@ -351,7 +343,7 @@ def _collect_dir(self, path_info, tree, **kwargs):
         # Sorting the list by path to ensure reproducibility
         return sorted(result, key=itemgetter(self.PARAM_RELPATH))
 
-    def _save_dir_info(self, dir_info, path_info):
+    def _save_dir_info(self, dir_info):
         hash_, tmp_info = self._get_dir_info_hash(dir_info)
         new_info = self.cache.tree.hash_to_path_info(hash_)
         if self.cache.changed_cache_file(hash_):
@@ -360,8 +352,6 @@ def _save_dir_info(self, dir_info, path_info):
                 tmp_info, new_info, mode=self.cache.CACHE_MODE
             )
 
-        if self.exists(path_info):
-            self.state.save(path_info, hash_)
         self.state.save(new_info, hash_)
 
         return hash_
diff --git a/dvc/version.py b/dvc/version.py
index c883b6a67e..02ef7104a2 100644
--- a/dvc/version.py
+++ b/dvc/version.py
@@ -6,7 +6,7 @@
 import os
 import subprocess
 
-_BASE_VERSION = "1.2.3"
+_BASE_VERSION = "1.3.1"
 
 
 def _generate_version(base_version):
diff --git a/setup.py b/setup.py
index da84576f16..b90e9b05af 100644
--- a/setup.py
+++ b/setup.py
@@ -105,9 +105,7 @@ def run(self):
 tests_requirements = [
     "wheel>=0.31.1",
     # Test requirements:
-    # https://github.com/pytest-dev/pytest/issues/7558
-    # FIXME: pylint complaining for pytest.mark.* on v6.0
-    "pytest>=4.6.0,<6.0",
+    "pytest>=6.0.1",
     "pytest-docker>=0.7.2",
     "pytest-timeout>=1.3.3",
     "pytest-cov>=2.6.1",
diff --git a/tests/func/test_commit.py b/tests/func/test_commit.py
index 6c91abff31..958a29c539 100644
--- a/tests/func/test_commit.py
+++ b/tests/func/test_commit.py
@@ -2,7 +2,9 @@
 
 import pytest
 
+from dvc.dependency.base import DependencyDoesNotExistError
 from dvc.dvcfile import PIPELINE_FILE
+from dvc.output.base import OutputDoesNotExistError
 from dvc.stage.exceptions import StageCommitError
 from dvc.utils.yaml import dump_yaml, load_yaml
 
@@ -86,6 +88,24 @@ def test_commit_no_exec(tmp_dir, dvc):
     assert dvc.status(stage.path) == {}
 
 
+def test_commit_no_exec_missing_dep(tmp_dir, dvc):
+    stage = dvc.run(
+        name="my", cmd="mycmd", deps=["dep"], outs=["out"], no_exec=True
+    )
+    assert dvc.status(stage.path)
+
+    with pytest.raises(DependencyDoesNotExistError):
+        dvc.commit(stage.path, force=True)
+
+
+def test_commit_no_exec_missing_out(tmp_dir, dvc):
+    stage = dvc.run(name="my", cmd="mycmd", outs=["out"], no_exec=True)
+    assert dvc.status(stage.path)
+
+    with pytest.raises(OutputDoesNotExistError):
+        dvc.commit(stage.path, force=True)
+
+
 def test_commit_pipeline_stage(tmp_dir, dvc, run_copy):
     tmp_dir.gen("foo", "foo")
     stage = run_copy("foo", "bar", no_commit=True, name="copy-foo-bar")
diff --git a/tests/func/test_remote.py b/tests/func/test_remote.py
index 35ce310f06..38196ffbdd 100644
--- a/tests/func/test_remote.py
+++ b/tests/func/test_remote.py
@@ -232,6 +232,24 @@ def test_modify_missing_remote(tmp_dir, dvc):
     assert main(["remote", "modify", "myremote", "user", "xxx"]) == 251
 
 
+def test_remote_modify_local_on_repo_config(tmp_dir, dvc):
+    assert main(["remote", "add", "myremote", "http://example.com/path"]) == 0
+    assert (
+        main(["remote", "modify", "myremote", "user", "xxx", "--local"]) == 0
+    )
+    assert dvc.config.load_one("local")["remote"]["myremote"] == {
+        "user": "xxx"
+    }
+    assert dvc.config.load_one("repo")["remote"]["myremote"] == {
+        "url": "http://example.com/path"
+    }
+    dvc.config.load()
+    assert dvc.config["remote"]["myremote"] == {
+        "url": "http://example.com/path",
+        "user": "xxx",
+    }
+
+
 def test_external_dir_resource_on_no_cache(tmp_dir, dvc, tmp_path_factory):
     # https://github.com/iterative/dvc/issues/2647, is some situations
     # (external dir dependency) cache is required to calculate dir md5
diff --git a/tests/func/test_tree.py b/tests/func/test_tree.py
index 93b671bd75..3ab93efc9b 100644
--- a/tests/func/test_tree.py
+++ b/tests/func/test_tree.py
@@ -217,7 +217,10 @@ def test_repotree_cache_save(tmp_dir, dvc, scm, erepo_dir, local_cloud):
     with erepo_dir.dvc.state:
         cache = dvc.cache.local
         with cache.tree.state:
-            cache.save(PathInfo(erepo_dir / "dir"), tree, None)
+            path_info = PathInfo(erepo_dir / "dir")
+            hash_info = cache.tree.save_info(path_info)
+            cache.save(path_info, tree, hash_info)
+
     for hash_ in expected:
         assert os.path.exists(cache.tree.hash_to_path_info(hash_))
 
diff --git a/tests/func/test_version.py b/tests/func/test_version.py
index c55955db40..753d53e6ee 100644
--- a/tests/func/test_version.py
+++ b/tests/func/test_version.py
@@ -16,7 +16,7 @@ def test_info_in_repo(scm_init, tmp_dir, caplog):
 
     assert main(["version"]) == 0
 
-    assert re.search(r"DVC version: \d+\.\d+\.\d+\+.*", caplog.text)
+    assert re.search(r"DVC version: \d+\.\d+\.\d+.*", caplog.text)
     assert re.search(r"Platform: Python \d\.\d\.\d on .*", caplog.text)
     assert re.search(r"Supports: .*", caplog.text)
     assert re.search(r"Cache types: .*", caplog.text)
@@ -60,7 +60,7 @@ def test_fs_info_in_repo(tmp_dir, dvc, caplog):
 def test_info_outside_of_repo(tmp_dir, caplog):
     assert main(["version"]) == 0
 
-    assert re.search(r"DVC version: \d+\.\d+\.\d+\+.*", caplog.text)
+    assert re.search(r"DVC version: \d+\.\d+\.\d+.*", caplog.text)
     assert re.search(r"Platform: Python \d\.\d\.\d on .*", caplog.text)
     assert re.search(r"Supports: .*", caplog.text)
     assert not re.search(r"Cache types: .*", caplog.text)